diff --git a/conf/modules.config b/conf/modules.config index e90c7304..ed977394 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -49,6 +49,29 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + withName: 'PICARD_COLLECTMULTIPLEMETRICS' { + publishDir = [ + path: { "${params.outdir}/picard_collectmultiplemetrics" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'SAMTOOLS_FAIDX' { + publishDir = [ + path: { "${params.outdir}/samtools_faidx" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'SAMTOOLS_INDEX' { + publishDir = [ + path: { "${params.outdir}/bwamem2_mem" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } withName: 'MULTIQC_GLOBAL' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } diff --git a/modules.json b/modules.json index 97910dd0..c96335d6 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bowtie2/build": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "bwamem2/index": { @@ -17,7 +17,7 @@ }, "bwamem2/mem": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2", "installed_by": ["modules"], "patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff" }, @@ -28,18 +28,18 @@ }, "fastqscreen/buildfromindex": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "fastqscreen/fastqscreen": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"], "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff" }, "multiqc": { "branch": "master", - "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", + "git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6", "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { @@ -49,7 +49,7 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] }, "samtools/index": { @@ -59,12 +59,12 @@ }, "seqfu/stats": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] }, "seqtk/sample": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml index e590f7ce..066ff52e 100644 --- a/modules/nf-core/bowtie2/build/environment.yml +++ b/modules/nf-core/bowtie2/build/environment.yml @@ -1,5 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bowtie2=2.5.2 + # renovate: datasource=conda depName=bioconda/bowtie2 + - bioconda::bowtie2=2.5.4 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.21 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.21 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 9e2e0e5e..fb7effec 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -4,8 +4,8 @@ process BOWTIE2_BUILD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bowtie2:2.5.2--py39h6fed5c7_0' : - 'biocontainers/bowtie2:2.5.2--py39h6fed5c7_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b41b403e81883126c3227fc45840015538e8e2212f13abc9ae84e4b98891d51c/data' : + 'community.wave.seqera.io/library/bowtie2_htslib_samtools_pigz:edeb13799090a2a6' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 2729a92e..3e83ecb4 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -25,9 +25,10 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: [] output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing reference information @@ -36,11 +37,14 @@ output: type: file description: Bowtie2 genome index files pattern: "*.bt2" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test b/modules/nf-core/bowtie2/build/tests/main.nf.test index 16376025..ee94c19c 100644 --- a/modules/nf-core/bowtie2/build/tests/main.nf.test +++ b/modules/nf-core/bowtie2/build/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test Process BOWTIE2_BUILD" - script "modules/nf-core/bowtie2/build/main.nf" + script "../main.nf" process "BOWTIE2_BUILD" tag "modules" tag "modules_nfcore" @@ -15,7 +15,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } diff --git a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap index 6875e021..ea5711e4 100644 --- a/modules/nf-core/bowtie2/build/tests/main.nf.test.snap +++ b/modules/nf-core/bowtie2/build/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ] ], "1": [ - "versions.yml:md5,1df11e9b82891527271c889c880d3974" + "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c" ], "index": [ [ @@ -36,10 +36,14 @@ ] ], "versions": [ - "versions.yml:md5,1df11e9b82891527271c889c880d3974" + "versions.yml:md5,d136fb9c16f0a9fb2ae804b2a5fbc09c" ] } ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.02.1" + }, "timestamp": "2023-11-23T11:51:01.107681997" } } \ No newline at end of file diff --git a/modules/nf-core/bowtie2/build/tests/tags.yml b/modules/nf-core/bowtie2/build/tests/tags.yml deleted file mode 100644 index 81aa61da..00000000 --- a/modules/nf-core/bowtie2/build/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bowtie2/build: - - modules/nf-core/bowtie2/build/** diff --git a/modules/nf-core/bwamem2/mem/bwamem2-mem.diff b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff new file mode 100644 index 00000000..be5074e8 --- /dev/null +++ b/modules/nf-core/bwamem2/mem/bwamem2-mem.diff @@ -0,0 +1,18 @@ +Changes in component 'nf-core/bwamem2/mem' +'modules/nf-core/bwamem2/mem/meta.yml' is unchanged +'modules/nf-core/bwamem2/mem/environment.yml' is unchanged +Changes in 'bwamem2/mem/main.nf': +--- modules/nf-core/bwamem2/mem/main.nf ++++ modules/nf-core/bwamem2/mem/main.nf +@@ -1,6 +1,6 @@ + process BWAMEM2_MEM { + tag "$meta.id" +- label 'process_high' ++ label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + +'modules/nf-core/bwamem2/mem/tests/main.nf.test' is unchanged +'modules/nf-core/bwamem2/mem/tests/main.nf.test.snap' is unchanged +************************************************************ diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index c069e281..f3637444 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -6,8 +6,8 @@ channels: dependencies: # renovate: datasource=conda depName=bioconda/bwa-mem2 - - bwa-mem2=2.2.1 + - bwa-mem2=2.3 # renovate: datasource=conda depName=bioconda/htslib - - htslib=1.21 + - htslib=1.22.1 # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.21 + - samtools=1.22.1 diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index eab662a8..e12a68b0 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -1,11 +1,11 @@ process BWAMEM2_MEM { tag "$meta.id" - label 'process_high' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9ac054213e67b3c9308e409b459080bbe438f8fd6c646c351bc42887f35a42e7/data' : - 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : + 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index ec90701f..b7d40a68 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -1,17 +1,17 @@ { "sarscov2 - [fastq1, fastq2], index, fasta, false": { "content": [ - "9505760d66e1d5a5d34ab79a98228c6", + "e414c2d48e2e44c2c52c20ecd88e8bd8", "57aeef88ed701a8ebc8e2f0a381b2a6", [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.7" }, - "timestamp": "2025-03-27T10:57:52.782442426" + "timestamp": "2025-09-23T11:44:52.73673293" }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "5": [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ], "bam": [ [ @@ -74,56 +74,56 @@ ], "versions": [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.7" }, - "timestamp": "2025-03-27T10:58:37.140104324" + "timestamp": "2025-09-23T11:45:14.834888709" }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ - "e0c38d5772ca5f4d5d9999f4477e933c", + "716ed1ef39deaad346ca7cf86e08f959", "af8628d9df18b2d3d4f6fd47ef2bb872", [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.7" }, - "timestamp": "2025-03-27T10:58:19.047052261" + "timestamp": "2025-09-23T11:45:04.750057645" }, "sarscov2 - fastq, index, fasta, false": { "content": [ - "58d05395bbb819e929885bde415947ae", + "283a83f604f3f5338acedfee349dccf4", "798439cbd7fd81cbcc5078022dc5479d", [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.7" }, - "timestamp": "2025-03-27T10:56:53.456559296" + "timestamp": "2025-09-23T11:44:28.57550711" }, "sarscov2 - fastq, index, fasta, true": { "content": [ - "276189f6f003f99a87664e74fad2893d", + "ed99048bb552cac58e39923b550b6d5b", "94fcf617f5b994584c4e8d4044e16b4f", [ - "versions.yml:md5,ca1b1dcf82b92fb0751816fca16a477a" + "versions.yml:md5,3574188ab1f33fd99cff9f5562dfb885" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.7" }, - "timestamp": "2025-03-27T10:57:21.949711746" + "timestamp": "2025-09-23T11:44:40.437183765" } } \ No newline at end of file diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml index 85764e0d..3b3ba521 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::fastq-screen=0.15.3" + - bioconda::fastq-screen=0.15.3 diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml index d92817fc..0291620b 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml @@ -17,23 +17,25 @@ tools: licence: ["GPL-3.0-or-later"] identifier: "" input: - - - genome_names: - type: string - description: List of names for each index - - - indexes: - type: directory - description: Bowtie2 genome directories containing index files + - genome_names: + type: string + description: List of names for each index + - indexes: + type: directory + description: Bowtie2 genome directories containing index files output: - - database: - - FastQ_Screen_Genomes: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + database: + - FastQ_Screen_Genomes: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap index 0fe7d7d1..a485079b 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap +++ b/modules/nf-core/fastqscreen/buildfromindex/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "database": { + "sarscov2 - human": { "content": [ [ [ @@ -21,25 +21,49 @@ ], "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265" ] + ], + [ + "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.02.1" }, - "timestamp": "2024-05-01T20:37:34.647221" + "timestamp": "2025-03-25T12:58:36.506586801" }, - "versions": { + "sarscov2 - human": { "content": [ + [ + [ + [ + "genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf", + "genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184", + "genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597" + ], + [ + "genome.1.bt2:md5,2fbc8eeaf480f03b3a2362a782fa5755", + "genome.2.bt2:md5,a5300e3cf590d4cd8bd5521cac6337d6", + "genome.3.bt2:md5,d2a7a0e1c9891e847a15781c0695b84e", + "genome.4.bt2:md5,a55dc4b09e3e00586de6963800c95b9a", + "genome.rev.1.bt2:md5,93c07f7d04e5da6bf1322ad5f46ac806", + "genome.rev.2.bt2:md5,c3fa30132c0c9b9bc7868059e8e23466" + ], + "fastq_screen.conf:md5,ca56e866c7006a46bdfe4e751e787265" + ] + ], [ "versions.yml:md5,c2bcf85b00046c72d5dccd2dba8ac35c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-05-01T20:37:35.126085" + "timestamp": "2025-03-25T08:34:46.992911211" }, "sarscov2 - human - stub": { "content": [ @@ -63,9 +87,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-05-01T20:39:14.913696" + "timestamp": "2025-03-25T08:35:14.073325807" } } \ No newline at end of file diff --git a/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml b/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml deleted file mode 100644 index 9c98e870..00000000 --- a/modules/nf-core/fastqscreen/buildfromindex/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqscreen/buildfromindex: - - "modules/nf-core/fastqscreen/buildfromindex/**" diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml index 7d4c8922..9ff968c9 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml @@ -6,9 +6,3 @@ channels: dependencies: - bioconda::fastq-screen=0.16.0 - bioconda::perl-gdgraph=1.54 - # - gzip - # - SAMtools - # - bowtie - # - bowtie2 - # - bwa - # - bismark diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff index 658d149b..c6fdd2f1 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff +++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff @@ -1,73 +1,90 @@ Changes in component 'nf-core/fastqscreen/fastqscreen' +'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged Changes in 'fastqscreen/fastqscreen/environment.yml': --- modules/nf-core/fastqscreen/fastqscreen/environment.yml +++ modules/nf-core/fastqscreen/fastqscreen/environment.yml -@@ -4,5 +4,11 @@ +@@ -4,5 +4,5 @@ - conda-forge - bioconda dependencies: -- - "bioconda::fastq-screen=0.15.3" +- - bioconda::fastq-screen=0.15.3 + - bioconda::fastq-screen=0.16.0 - bioconda::perl-gdgraph=1.54 -+ # - gzip -+ # - SAMtools -+ # - bowtie -+ # - bowtie2 -+ # - bwa -+ # - bismark Changes in 'fastqscreen/fastqscreen/main.nf': --- modules/nf-core/fastqscreen/fastqscreen/main.nf +++ modules/nf-core/fastqscreen/fastqscreen/main.nf -@@ -4,12 +4,12 @@ +@@ -1,22 +1,22 @@ + process FASTQSCREEN_FASTQSCREEN { +- tag "$meta.id" ++ tag "${meta.id}" + label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastq-screen:0.15.3--pl5321hdfd78af_0': - 'biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' : -+ 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}" ++ container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ++ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' ++ : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}" input: - tuple val(meta), path(reads) // .fastq files - path database + tuple val(meta), path(reads, arity: '1..2') -+ tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners) ++ tuple val(ref_names), path(ref_dirs, name: "ref*"), val(ref_basenames), val(ref_aligners) output: - tuple val(meta), path("*.txt") , emit: txt -@@ -24,31 +24,42 @@ +- tuple val(meta), path("*.txt") , emit: txt +- tuple val(meta), path("*.png") , emit: png , optional: true +- tuple val(meta), path("*.html") , emit: html ++ tuple val(meta), path("*.txt"), emit: txt ++ tuple val(meta), path("*.png"), emit: png, optional: true ++ tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true +- path "versions.yml" , emit: versions ++ path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when +@@ -24,31 +24,46 @@ script: def prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: "" + def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n') + // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2' -+ def num_reads = reads instanceof List ? reads.size() : 1 ++ def num_reads = reads instanceof List ? reads.size() : 1 + def file_extensions = ['txt', 'html', 'png'] -+ def mv_cmd = file_extensions.collect { ext -> -+ reads.withIndex().collect { read, i -> -+ "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}" -+ }.join(' && ') -+ }.join(' && ') ++ def mv_cmd = file_extensions ++ .collect { ext -> ++ reads ++ .withIndex() ++ .collect { read, i -> ++ "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i + 1}" : ''}_screen.${ext}" ++ } ++ .join(' && ') ++ } ++ .join(' && ') """ - fastq_screen --threads ${task.cpus} \\ - --aligner bowtie2 \\ - --conf ${database}/fastq_screen.conf \\ -+ echo '${config_content}' > fastq_screen.conf -+ -+ fastq_screen \\ -+ --conf fastq_screen.conf \\ -+ --threads ${task.cpus} \\ - $reads \\ +- $reads \\ - $args \\ -+ $args ++ echo '${config_content}' > fastq_screen.conf - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//') - END_VERSIONS -+ $mv_cmd ++ fastq_screen \\ ++ --conf fastq_screen.conf \\ ++ --threads ${task.cpus} \\ ++ ${reads} \\ ++ ${args} ++ ++ ${mv_cmd} + + fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//') + echo "\\\"${task.process}\\\":" > versions.yml @@ -92,12 +109,10 @@ Changes in 'fastqscreen/fastqscreen/main.nf': + echo "\\\"${task.process}\\\":" > versions.yml + echo " fastqscreen: \$fastq_screen_version" >> versions.yml """ - +- } -'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged -'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged -'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged +'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf index 21012c1f..dc53ae21 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/main.nf +++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf @@ -1,22 +1,22 @@ process FASTQSCREEN_FASTQSCREEN { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' : - 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fc/fc53eee7ca23c32220a9662fbb63c67769756544b6d74a1ee85cf439ea79a7ee/data' + : 'community.wave.seqera.io/library/fastq-screen_perl-gdgraph:5c1786a5d5bc1309'}" input: tuple val(meta), path(reads, arity: '1..2') - tuple val(ref_names), path(ref_dirs, name:"ref*"), val(ref_basenames), val(ref_aligners) + tuple val(ref_names), path(ref_dirs, name: "ref*"), val(ref_basenames), val(ref_aligners) output: - tuple val(meta), path("*.txt") , emit: txt - tuple val(meta), path("*.png") , emit: png , optional: true - tuple val(meta), path("*.html") , emit: html + tuple val(meta), path("*.txt"), emit: txt + tuple val(meta), path("*.png"), emit: png, optional: true + tuple val(meta), path("*.html"), emit: html tuple val(meta), path("*.fastq.gz"), emit: fastq, optional: true - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -27,23 +27,28 @@ process FASTQSCREEN_FASTQSCREEN { def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n') // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2' - def num_reads = reads instanceof List ? reads.size() : 1 + def num_reads = reads instanceof List ? reads.size() : 1 def file_extensions = ['txt', 'html', 'png'] - def mv_cmd = file_extensions.collect { ext -> - reads.withIndex().collect { read, i -> - "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}" - }.join(' && ') - }.join(' && ') + def mv_cmd = file_extensions + .collect { ext -> + reads + .withIndex() + .collect { read, i -> + "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i + 1}" : ''}_screen.${ext}" + } + .join(' && ') + } + .join(' && ') """ echo '${config_content}' > fastq_screen.conf fastq_screen \\ --conf fastq_screen.conf \\ --threads ${task.cpus} \\ - $reads \\ - $args + ${reads} \\ + ${args} - $mv_cmd + ${mv_cmd} fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//') echo "\\\"${task.process}\\\":" > versions.yml @@ -61,5 +66,4 @@ process FASTQSCREEN_FASTQSCREEN { echo "\\\"${task.process}\\\":" > versions.yml echo " fastqscreen: \$fastq_screen_version" >> versions.yml """ - } diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml index 39c86b4f..81e15b02 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml @@ -29,50 +29,58 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - - database: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" + ontologies: [] + - database: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" output: - - txt: - - meta: + txt: + - - meta: type: map description: Groovy Map containing sample information - "*.txt": type: file description: TXT file containing alignment statistics pattern: "*.txt" - - png: - - meta: + ontologies: [] + png: + - - meta: type: map description: Groovy Map containing sample information - "*.png": type: file description: PNG file with graphical representation of alignments pattern: "*.png" - - html: - - meta: + ontologies: [] + html: + - - meta: type: map description: Groovy Map containing sample information - "*.html": type: file - description: HTML file containing mapping results as a table and graphical representation + description: HTML file containing mapping results as a table and graphical + representation pattern: "*.html" - - fastq: - - meta: + ontologies: [] + fastq: + - - meta: type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + description: Groovy Map containing sample information - "*.fastq.gz": type: file - description: FastQ file containing reads that did not align to any database (optional) + description: FastQ file containing reads that did not align to any database + (optional) pattern: "*.fastq.gz" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap index 2afffdea..042f3bb4 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap +++ b/modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap @@ -124,9 +124,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-08-31T05:45:54.845041829" + "timestamp": "2025-03-25T08:38:33.98646086" } } \ No newline at end of file diff --git a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml b/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml deleted file mode 100644 index b03bfb45..00000000 --- a/modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqscreen/fastqscreen: - - "modules/nf-core/fastqscreen/fastqscreen/**" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index c1158fb0..5d0780af 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -52,6 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data + touch multiqc_data/.stub mkdir multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 64219b7d..a505abc1 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -216,4 +216,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/seqfu/stats/environment.yml b/modules/nf-core/seqfu/stats/environment.yml index 8fa07dfc..210e292b 100644 --- a/modules/nf-core/seqfu/stats/environment.yml +++ b/modules/nf-core/seqfu/stats/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::seqfu=1.20.3" + - bioconda::seqfu=1.22.3 diff --git a/modules/nf-core/seqfu/stats/main.nf b/modules/nf-core/seqfu/stats/main.nf index 0f8bb3e2..ced2451c 100644 --- a/modules/nf-core/seqfu/stats/main.nf +++ b/modules/nf-core/seqfu/stats/main.nf @@ -4,18 +4,17 @@ process SEQFU_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqfu:1.20.3--h1eb128b_0': - 'biocontainers/seqfu:1.20.3--h1eb128b_0' }" - + 'https://depot.galaxyproject.org/singularity/seqfu:1.22.3--hfd12232_2': + 'biocontainers/seqfu:1.22.3--hfd12232_2' }" input: // stats can get one or more fasta or fastq files tuple val(meta), path(files) output: - tuple val(meta), path("*.tsv") , emit: stats + tuple val(meta), path("*.tsv") , emit: stats tuple val(meta), path("*_mqc.txt"), emit: multiqc - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -40,12 +39,14 @@ process SEQFU_STATS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ + echo $args + + touch ${prefix}.tsv touch ${prefix}_mqc.txt - seqfu stats ${prefix}_mqc.txt > ${prefix}.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": - seqfu: \$(samtools --version |& sed '1!d ; s/samtools //') + seqfu: \$(seqfu version) END_VERSIONS """ } diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml index f534a3f5..573498c5 100644 --- a/modules/nf-core/seqfu/stats/meta.yml +++ b/modules/nf-core/seqfu/stats/meta.yml @@ -27,10 +27,12 @@ input: type: file description: One or more FASTA or FASTQ files pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ output: #Only when we have meta - - stats: - - meta: + stats: + - - meta: type: map description: | Groovy Map containing sample information @@ -39,8 +41,10 @@ output: type: file description: Tab-separated output file with basic sequence statistics. pattern: "*.{tsv}" - - multiqc: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + multiqc: + - - meta: type: map description: | Groovy Map containing sample information @@ -49,11 +53,14 @@ output: type: file description: MultiQC ready table pattern: "*.{_mqc.txt}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@telatin" maintainers: diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test b/modules/nf-core/seqfu/stats/tests/main.nf.test index b889b2bb..3d13b05b 100644 --- a/modules/nf-core/seqfu/stats/tests/main.nf.test +++ b/modules/nf-core/seqfu/stats/tests/main.nf.test @@ -9,14 +9,13 @@ nextflow_process { tag "seqfu" tag "seqfu/stats" - test("seqfu stats - faa") { // test with 1 FAA file (with multiple sequences of different length) when { process { """ input[0] = [ - [ id:'test' ], + [ id:'test_faa' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ] """ @@ -26,12 +25,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.stats }, - { assert process.out.multiqc }, - { assert process.out.stats.size() == 1 }, - { assert snapshot(process.out.versions).match("versions-single") }, - { assert snapshot(process.out.stats).match("stats-single") }, - { assert path(process.out.stats.get(0).get(1)).md5 == "26141ef87ad8a6f59a6f283cc0a06fda" } + { assert snapshot(process.out).match() } ) } @@ -43,7 +37,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], + [ id:'test_multiple' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), @@ -58,15 +52,34 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.stats }, - { assert process.out.multiqc }, - { assert process.out.stats.size() == 1 }, - { assert path(process.out.versions[0]).readLines()[1].contains('.') }, - { assert snapshot(process.out.stats).match("stats-multi") }, - { assert snapshot(process.out.stats).md5().match("multi-lines") }, - { assert path(process.out.stats[0][1]).readLines()[0] == 'File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax' }, - { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('genome.fasta') }, - { assert path(process.out.multiqc[0][1]).readLines().join('\n').contains('proteome.fasta') } + { assert snapshot(process.out).match() } + ) + } + + } + + test("seqfu stats - faa - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test_stub' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success}, + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } ) } diff --git a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap index 8049c827..30b16993 100644 --- a/modules/nf-core/seqfu/stats/tests/main.nf.test.snap +++ b/modules/nf-core/seqfu/stats/tests/main.nf.test.snap @@ -1,56 +1,156 @@ { - "versions-single": { + "seqfu stats - faa - stub": { "content": [ + { + "0": [ + [ + { + "id": "test_stub" + }, + "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test_stub" + }, + "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" + ], + "multiqc": [ + [ + { + "id": "test_stub" + }, + "test_stub_mqc.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test_stub" + }, + "test_stub.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" + ] + }, [ - "versions.yml:md5,fd11b4665f68f22e7ad4c646ad3c56cd" + { + "SEQFU_STATS": { + "seqfu": "1.22.3" + } + } ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-19T20:21:50.896221522" - }, - "multi-lines": { - "content": "d5ab14ce74939f856edc64c6a8d250d3", - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-19T20:22:03.775940585" + "timestamp": "2025-09-24T12:51:50.35812127" }, - "stats-single": { + "seqfu stats - faa": { "content": [ - [ - [ - { - "id": "test" - }, - "test.tsv:md5,26141ef87ad8a6f59a6f283cc0a06fda" + { + "0": [ + [ + { + "id": "test_faa" + }, + "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04" + ] + ], + "1": [ + [ + { + "id": "test_faa" + }, + "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c" + ] + ], + "2": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" + ], + "multiqc": [ + [ + { + "id": "test_faa" + }, + "test_faa_mqc.txt:md5,8f3c2edaf1ea5be912c9f99b21b2856c" + ] + ], + "stats": [ + [ + { + "id": "test_faa" + }, + "test_faa.tsv:md5,0d6bf2cc788f7828761440a1689cac04" + ] + ], + "versions": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-19T20:21:50.937732021" + "timestamp": "2025-09-24T12:52:03.19664223" }, - "stats-multi": { + "seqfu stats - multiple files": { "content": [ - [ - [ - { - "id": "test" - }, - "test.tsv:md5,98102573ecf7e3b9e53db1c6e0f02b06" + { + "0": [ + [ + { + "id": "test_multiple" + }, + "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae" + ] + ], + "1": [ + [ + { + "id": "test_multiple" + }, + "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445" + ] + ], + "2": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" + ], + "multiqc": [ + [ + { + "id": "test_multiple" + }, + "test_multiple_mqc.txt:md5,dbc6e762eebbf756cd0687807de60445" + ] + ], + "stats": [ + [ + { + "id": "test_multiple" + }, + "test_multiple.tsv:md5,d016de3d84187a06c8e19b8dabccb3ae" + ] + ], + "versions": [ + "versions.yml:md5,7e7581ee4a87fd1f9969628ae050e689" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-19T20:22:03.681146614" + "timestamp": "2025-09-24T12:52:11.315174611" } } \ No newline at end of file diff --git a/modules/nf-core/seqfu/stats/tests/tags.yml b/modules/nf-core/seqfu/stats/tests/tags.yml deleted file mode 100644 index 2685ed43..00000000 --- a/modules/nf-core/seqfu/stats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -seqfu/stats: - - "modules/nf-core/seqfu/stats/**" diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml index 693aa5c1..b1d11cbd 100644 --- a/modules/nf-core/seqtk/sample/environment.yml +++ b/modules/nf-core/seqtk/sample/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index ea9b839e..0c2aaeda 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -20,7 +20,7 @@ process SEQTK_SAMPLE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - if (!(args ==~ /.*-s[0-9]+.*/)) { + if (!(args ==~ /.*\ -s\ ?[0-9]+.*/)) { args += " -s100" } if ( !sample_size ) { diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml index 42f67d8f..ed1f3325 100644 --- a/modules/nf-core/seqtk/sample/meta.yml +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -23,12 +23,13 @@ input: type: file description: List of input FastQ files pattern: "*.{fastq.gz}" + ontologies: [] - sample_size: - type: integer - description: Number of reads to sample. + type: float + description: Fraction (<1.0) or number (>=1) of reads to sample. output: - - reads: - - meta: + reads: + - - meta: type: map description: | Groovy Map containing sample information @@ -37,11 +38,14 @@ output: type: file description: Subsampled FastQ files pattern: "*.{fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@kaurravneet4123" - "@sidorov-si" diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test index c121c9d9..2152ecd4 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test @@ -77,4 +77,26 @@ nextflow_process { } } + test("sarscov2_sample_singleend_frac") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + 0.5 + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap index a9fec3c4..aa6991e6 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap @@ -91,5 +91,36 @@ } ], "timestamp": "2024-02-22T15:58:29.474491" + }, + "sarscov2_sample_singleend_frac": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" + ] + ], + "1": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" + ] + ], + "versions": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ] + } + ], + "timestamp": "2025-07-15T09:48:30.275951" } } \ No newline at end of file diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config index b2dd4b9f..8d1db62f 100644 --- a/modules/nf-core/seqtk/sample/tests/standard.config +++ b/modules/nf-core/seqtk/sample/tests/standard.config @@ -3,4 +3,4 @@ process { ext.args = '-s100' ext.prefix = { "${meta.id}.sampled" } } -} \ No newline at end of file +} diff --git a/modules/nf-core/seqtk/sample/tests/tags.yml b/modules/nf-core/seqtk/sample/tests/tags.yml deleted file mode 100644 index e5d113b8..00000000 --- a/modules/nf-core/seqtk/sample/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -seqtk/sample: - - "modules/nf-core/seqtk/sample/**" diff --git a/nextflow_schema.json b/nextflow_schema.json index 52bb676f..4a7be1c8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -51,7 +51,7 @@ "skip_tools": { "type": "string", "description": "Comma-separated string of tools to skip", - "pattern": "^((fastqc|fastqscreen|seqfu_stats|seqtk_sample|bwamem2_index|bwamem2_mem)?,?)*(?\n \n \n \"nf-core/seqinspector\"\n \n\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/seqinspector)\n[![GitHub Actions CI Status](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/seqinspector/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/seqinspector)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23seqinspector-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/seqinspector)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/seqinspector** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Subsample reads ([`Seqtk`](https://github.com/lh3/seqtk))\n2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/seqinspector \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/seqinspector/usage) and the [parameter documentation](https://nf-co.re/seqinspector/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/seqinspector/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/seqinspector/output).\n\n## Credits\n\nnf-core/seqinspector was originally written by the Swedish [@NationalGenomicsInfrastructure](https://github.com/NationalGenomicsInfrastructure/).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [@mahesh-panchal](https://github.com/mahesh-panchal)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#seqinspector` channel](https://nfcore.slack.com/channels/seqinspector) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b" + "@id": "#71038893-a262-4eae-bd98-7ea776c53d1b" } ], "name": "nf-core/seqinspector" @@ -127,21 +127,21 @@ "ComputationalWorkflow" ], "creator": [ - { - "@id": "https://orcid.org/0000-0003-1675-0677" - }, { "@id": "https://orcid.org/0000-0003-2702-1103" }, { - "@id": "#89784800+kedhammar@users.noreply.github.com" + "@id": "https://orcid.org/0000-0003-1675-0677" }, { "@id": "https://orcid.org/0009-0004-5536-7210" + }, + { + "@id": "#89784800+kedhammar@users.noreply.github.com" } ], "dateCreated": "", - "dateModified": "2025-11-07T10:27:51Z", + "dateModified": "2025-11-19T12:42:42Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -182,11 +182,11 @@ "version": "!>=25.04.0" }, { - "@id": "#fbe02af1-e9dc-458e-a6f1-649522b5321b", + "@id": "#71038893-a262-4eae-bd98-7ea776c53d1b", "@type": "TestSuite", "instance": [ { - "@id": "#56ac1623-4e68-4598-9703-f769123f08c5" + "@id": "#993ccba2-3cbf-4d2d-9b44-21757f3c0ac7" } ], "mainEntity": { @@ -195,7 +195,7 @@ "name": "Test suite for nf-core/seqinspector" }, { - "@id": "#56ac1623-4e68-4598-9703-f769123f08c5", + "@id": "#993ccba2-3cbf-4d2d-9b44-21757f3c0ac7", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/seqinspector", "resource": "repos/nf-core/seqinspector/actions/workflows/nf-test.yml", @@ -323,6 +323,12 @@ "name": "nf-core", "url": "https://nf-co.re/" }, + { + "@id": "https://orcid.org/0000-0003-2702-1103", + "@type": "Person", + "email": "adrien.coulier@medsci.uu.se", + "name": "Adrien Coulier" + }, { "@id": "https://orcid.org/0000-0003-1675-0677", "@type": "Person", @@ -330,22 +336,16 @@ "name": "Mahesh Binzer-Panchal" }, { - "@id": "https://orcid.org/0000-0003-2702-1103", + "@id": "https://orcid.org/0009-0004-5536-7210", "@type": "Person", - "email": "adrien.coulier@medsci.uu.se", - "name": "Adrien Coulier" + "email": "agrimabhatt@Mac.home", + "name": "Agrima Bhatt" }, { "@id": "#89784800+kedhammar@users.noreply.github.com", "@type": "Person", "email": "89784800+kedhammar@users.noreply.github.com", "name": "Alfred Kedhammar" - }, - { - "@id": "https://orcid.org/0009-0004-5536-7210", - "@type": "Person", - "email": "agrimabhatt@n141-p117.eduroam.kth.se", - "name": "Agrima Bhatt" } ] } \ No newline at end of file diff --git a/tests/.nftignore b/tests/.nftignore index e5098397..ee3b4013 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -11,4 +11,11 @@ multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.t multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/{global_report,group_reports/*}/multiqc_report.html +picard_collectmultiplemetrics/*.pdf +picard_collectmultiplemetrics/*_metrics +picard_collectmultiplemetrics/alignment_summary_metrics +picard_collectmultiplemetrics/base_distribution_by_cycle_metrics +picard_collectmultiplemetrics/quality_by_cycle_metrics +picard_collectmultiplemetrics/quality_distribution_metrics +picard_collectmultiplemetrics/*_summary_metrics pipeline_info/*.{html,json,txt,yml} diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap index 885a1e7a..927e3419 100644 --- a/tests/MiSeq.main.nf.test.snap +++ b/tests/MiSeq.main.nf.test.snap @@ -39,7 +39,7 @@ }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", - "samtools": 1.21 + "samtools": "1.22.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -47,8 +47,17 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "Workflow": { "nf-core/seqinspector": "v1.0dev" @@ -64,6 +73,7 @@ "bwamem2_index/bwamem2/genome.fa.pac", "bwamem2_mem", "bwamem2_mem/SAMPLE_SINGLE_END_1.bam", + "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai", "fastqc", "fastqc/SAMPLE_SINGLE_END_1_fastqc.html", "fastqc/SAMPLE_SINGLE_END_1_fastqc.zip", @@ -93,9 +103,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -110,6 +137,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -124,6 +161,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -138,10 +185,32 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", "seqfu_stats", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt" @@ -152,7 +221,8 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85", + "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b", + "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616", "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5", "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f", @@ -168,16 +238,35 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607", "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8", - "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702", - "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb", - "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39" + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99", + "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942", + "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703", + "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703", + "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0", + "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627", + "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023", + "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9", + "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af", + "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876", + "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c", + "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:23:17.145777453" + "timestamp": "2025-11-19T12:16:11.695977259" }, "Miseq data test (skip fastqc)": { "content": [ @@ -187,13 +276,22 @@ }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", - "samtools": 1.21 + "samtools": "1.22.1" }, "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "Workflow": { "nf-core/seqinspector": "v1.0dev" @@ -209,6 +307,7 @@ "bwamem2_index/bwamem2/genome.fa.pac", "bwamem2_mem", "bwamem2_mem/SAMPLE_SINGLE_END_1.bam", + "bwamem2_mem/SAMPLE_SINGLE_END_1.bam.bai", "fastqscreen", "fastqscreen/SAMPLE_SINGLE_END_1_screen.html", "fastqscreen/SAMPLE_SINGLE_END_1_screen.png", @@ -223,25 +322,84 @@ "multiqc/global_report/multiqc_data/multiqc_citations.txt", "multiqc/global_report/multiqc_data/multiqc_data.json", "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_SINGLE_END_1.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", "seqfu_stats", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu.tsv", "seqfu_stats/SAMPLE_SINGLE_END_1_seqfu_mqc.txt" @@ -252,21 +410,41 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "SAMPLE_SINGLE_END_1.bam:md5,79744f146752fd486b09604be721cc85", + "SAMPLE_SINGLE_END_1.bam:md5,ff8893272a6560cac7067fd8a9406f9b", + "SAMPLE_SINGLE_END_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "SAMPLE_SINGLE_END_1_screen.png:md5,ad98ae0f39335aede67e0a233cf16616", "SAMPLE_SINGLE_END_1_screen.txt:md5,588b1b1f2d307fae7272ab0819e4bac5", "fastq_screen_plot.txt:md5,8393eabda6ebac90ff00533f9562271f", "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,bd50a8641c6481cc497fc6e3e9af2607", - "multiqc_seqfu.txt:md5,8e6989a2392f599a09a5c3edf8119702", - "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,f65c868e562291647d539090698ba5eb", - "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,1de529f1e2cbd4df0945cb08a24d6d39" + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fe082d3b5dcc3d338e25bc027e17dc99", + "multiqc_picard_baseContent.txt:md5,796e8e0803ad3ed4fd1c76f073784942", + "multiqc_picard_quality_by_cycle.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "multiqc_picard_quality_score_distribution.txt:md5,bad70b98811c4cbe4728f53334993703", + "multiqc_seqfu.txt:md5,7ec63bc3465b3fc8e316e2443ec4c848", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,d1e7814f9a612561dcbeafb9d8c887f1", + "picard_QualityScoreDistribution_histogram.txt:md5,bad70b98811c4cbe4728f53334993703", + "picard_alignment_readlength_plot.txt:md5,0fe7e17f1c58b7a6291bc1ff80fdfaa0", + "picard_alignment_summary.txt:md5,c770d3ee98dadaee77ef43967a974627", + "picard_base_distribution_by_cycle__Adenine.txt:md5,65d43b083e90830aa9451bde65a261b8", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,31dc4f314d8e3f8e086e7ae761638023", + "picard_base_distribution_by_cycle__Guanine.txt:md5,d92fac15687942c0f9c436ba0cf55fc9", + "picard_base_distribution_by_cycle__Thymine.txt:md5,00b76f45bbfc9acd2774f90612e53333", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,5451af67007a16e7645d0393011414af", + "picard_quality_by_cycle.txt:md5,46fbe44a9788f2e9184e2c1d689c2876", + "picard_quality_score_distribution.txt:md5,154ee2704c7adad6b26877da26fe6b77", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_SINGLE_END_1_seqfu.tsv:md5,33a9e44386f308d43881a58394b6b17c", + "SAMPLE_SINGLE_END_1_seqfu_mqc.txt:md5,e67e819605ab49182aacf1d676dc885d" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:47:45.83823672" + "timestamp": "2025-11-19T12:16:53.917262693" } } \ No newline at end of file diff --git a/tests/MiSeq_PairedEnd.main.nf.test.snap b/tests/MiSeq_PairedEnd.main.nf.test.snap index 10a9b11a..4b17b6aa 100644 --- a/tests/MiSeq_PairedEnd.main.nf.test.snap +++ b/tests/MiSeq_PairedEnd.main.nf.test.snap @@ -7,7 +7,7 @@ }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", - "samtools": 1.21 + "samtools": "1.22.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -15,8 +15,17 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "Workflow": { "nf-core/seqinspector": "v1.0dev" @@ -32,7 +41,9 @@ "bwamem2_index/bwamem2/genome.fa.pac", "bwamem2_mem", "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam", + "bwamem2_mem/SAMPLE_PAIRED_END_1_1.bam.bai", "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam", + "bwamem2_mem/SAMPLE_PAIRED_END_2_2.bam.bai", "fastqc", "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.html", "fastqc/SAMPLE_PAIRED_END_1_1_1_fastqc.zip", @@ -76,9 +87,27 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Bases.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary_Aligned_Reads.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -92,6 +121,18 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -105,6 +146,18 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -118,6 +171,18 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -141,9 +206,27 @@ "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/Bpacificus/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Bases.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_alignment_summary_Aligned_Reads.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/Bpacificus/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/Bpacificus/multiqc_plots", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -157,6 +240,18 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-cnt.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Bases-pct.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-cnt.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/Bpacificus/multiqc_plots/png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -170,6 +265,18 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-cnt.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Bases-pct.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-cnt.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_alignment_summary_Aligned_Reads-pct.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/Bpacificus/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/Bpacificus/multiqc_plots/png/seqfu.png", "multiqc/group_reports/Bpacificus/multiqc_plots/svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -183,10 +290,42 @@ "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-cnt.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Bases-pct.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-cnt.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/Bpacificus/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/Bpacificus/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/Bpacificus/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SAMPLE_PAIRED_END_2_2.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", "seqfu_stats", "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu.tsv", "seqfu_stats/SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt", @@ -199,8 +338,10 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "SAMPLE_PAIRED_END_1_1.bam:md5,ced6a17fb3dee760c2606860e1177071", - "SAMPLE_PAIRED_END_2_2.bam:md5,15ada2a4f4a6cf2978aeaeb64a525197", + "SAMPLE_PAIRED_END_1_1.bam:md5,44c0ef738b73e26f67ded45ca4cb9e5b", + "SAMPLE_PAIRED_END_1_1.bam.bai:md5,82724835c47f8e1d1a86e13ef469b464", + "SAMPLE_PAIRED_END_2_2.bam:md5,9e20db3f3088fc478c223839e3a4ed62", + "SAMPLE_PAIRED_END_2_2.bam.bai:md5,3c4bdff0f906f2234fdeee8eea719210", "SAMPLE_PAIRED_END_1_1_1_screen.png:md5,f52ddd0e65f23f68dd8d58d5453417db", "SAMPLE_PAIRED_END_1_1_1_screen.txt:md5,921b08eeb461a2aa1bd42bba53900f70", "SAMPLE_PAIRED_END_1_1_2_screen.png:md5,908f4fceea8aa546106efdaa7ca78f7d", @@ -222,7 +363,25 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5", "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984", - "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb", + "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f", + "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0", + "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0", + "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712", + "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792", + "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170", + "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d", + "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6", + "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e", + "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d", "fastq_screen_plot.txt:md5,642264b93871c724aaa5d38b91c752dd", "fastqc-status-check-heatmap.txt:md5,8e29ad6b23e03267c33bd9ed3385a44b", "fastqc_adapter_content_plot.txt:md5,46fbd727a4996a3f0310d0423c628445", @@ -236,17 +395,37 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,5ef00028497d3271c9f0ea9a961db1e5", "multiqc_fastqc.txt:md5,bc499ad273fd1c887056c31b82544984", - "multiqc_seqfu.txt:md5,1f1e063e4a509a26cee167c3b20389c0", - "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,bbd911ff3fa43212dfd4c5a5872dbdb6", - "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,cd60f746b6749cc66213d031af1b931c", - "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,152566a128dd657da33465b4966b5799", - "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,8a3296956e094e3a95e28431e6009c40" + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,35d289ee535a0442db72a65391f375eb", + "multiqc_picard_baseContent.txt:md5,72b0ae83ed58052bfd768021d377c78f", + "multiqc_picard_quality_by_cycle.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "multiqc_picard_quality_score_distribution.txt:md5,99be409e325619171b820d762dd023c0", + "multiqc_seqfu.txt:md5,139354afd154804b4b77f997277f3ee9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,f6514f14befb874ded5aed79caba3e7b", + "picard_QualityScoreDistribution_histogram.txt:md5,99be409e325619171b820d762dd023c0", + "picard_alignment_readlength_plot.txt:md5,4172702f791d043135f21e3a227fe712", + "picard_alignment_summary_Aligned_Bases.txt:md5,a166c14210e17d3541482b500443f792", + "picard_alignment_summary_Aligned_Reads.txt:md5,c5e5228e85ffb2182274d641ffa6743f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,3fe18f1144eb85f9206d1bee4eb11bb3", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,2e1383b692e76f4b915ccbe9bb9b9170", + "picard_base_distribution_by_cycle__Guanine.txt:md5,2a595bc9ac547f3b5224a57a6b0a127d", + "picard_base_distribution_by_cycle__Thymine.txt:md5,157ea873dd2faff46efdd62f7f6aa84c", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,98f4e5ed094b41eb131d493b4f06bcd6", + "picard_quality_by_cycle.txt:md5,2634f306a33f648bac74bc7cd3253f9e", + "picard_quality_score_distribution.txt:md5,ecde9f0e859a6eecc5cea75a156c632d", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "SAMPLE_PAIRED_END_1_1_seqfu.tsv:md5,be29dfe848eab9a10ee0d46691223eae", + "SAMPLE_PAIRED_END_1_1_seqfu_mqc.txt:md5,0aca00c7f64454af520c7e08ec595d2b", + "SAMPLE_PAIRED_END_2_2_seqfu.tsv:md5,44a5cb826e001d58208a5855938fa82b", + "SAMPLE_PAIRED_END_2_2_seqfu_mqc.txt:md5,ac1740de9ef142c99c993fa9824ead63" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:24:43.782493978" + "timestamp": "2025-11-19T12:18:12.497819256" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap index f2985aa3..9b96d508 100644 --- a/tests/NovaSeq6000.main.nf.test.snap +++ b/tests/NovaSeq6000.main.nf.test.snap @@ -7,7 +7,7 @@ }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", - "samtools": 1.21 + "samtools": "1.22.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -15,8 +15,17 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "Workflow": { "nf-core/seqinspector": "v1.0dev" @@ -32,10 +41,15 @@ "bwamem2_index/bwamem2/genome.fa.pac", "bwamem2_mem", "bwamem2_mem/Sample1_1.bam", + "bwamem2_mem/Sample1_1.bam.bai", "bwamem2_mem/Sample23_3.bam", + "bwamem2_mem/Sample23_3.bam.bai", "bwamem2_mem/SampleA_2.bam", + "bwamem2_mem/SampleA_2.bam.bai", "bwamem2_mem/Undetermined_5.bam", + "bwamem2_mem/Undetermined_5.bam.bai", "bwamem2_mem/sampletest_4.bam", + "bwamem2_mem/sampletest_4.bam.bai", "fastqc", "fastqc/Sample1_1_fastqc.html", "fastqc/Sample1_1_fastqc.zip", @@ -86,9 +100,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -104,6 +135,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -119,6 +160,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -134,6 +185,16 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -159,9 +220,26 @@ "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -177,6 +255,16 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group1/multiqc_plots/png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -192,6 +280,16 @@ "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group1/multiqc_plots/svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -207,6 +305,16 @@ "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", @@ -231,9 +339,26 @@ "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -249,6 +374,16 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group2/multiqc_plots/png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -264,6 +399,16 @@ "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group2/multiqc_plots/svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -279,6 +424,16 @@ "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", @@ -303,9 +458,26 @@ "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -321,6 +493,16 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -336,6 +518,16 @@ "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/lane1/multiqc_plots/svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -351,6 +543,16 @@ "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", @@ -375,9 +577,26 @@ "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -393,6 +612,16 @@ "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/test/multiqc_plots/png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -408,6 +637,16 @@ "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu.png", "multiqc/group_reports/test/multiqc_plots/svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -423,10 +662,64 @@ "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/test/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", "seqfu_stats", "seqfu_stats/Sample1_1_seqfu.tsv", "seqfu_stats/Sample1_1_seqfu_mqc.txt", @@ -445,11 +738,16 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "Sample1_1.bam:md5,1efd4f55b836f732ccc3600697ebb4c3", - "Sample23_3.bam:md5,a13dd5db6ef2639f2227b6d3f9c92386", - "SampleA_2.bam:md5,c5082847134e5a1c0c869b2378637754", - "Undetermined_5.bam:md5,3453bb37bc50105e79f7bba23cbab9c5", - "sampletest_4.bam:md5,72532967a589a0a63e93ce86cf79f101", + "Sample1_1.bam:md5,93a7383f6e9a975ba87b315d435ecf18", + "Sample1_1.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "Sample23_3.bam:md5,e1003696a9e3501e122ca584e9a3c519", + "Sample23_3.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "SampleA_2.bam:md5,60f5dd83705aba4edbf460225116b824", + "SampleA_2.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "Undetermined_5.bam:md5,9f1a50be15a6504a5b03deec4645a419", + "Undetermined_5.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", + "sampletest_4.bam:md5,6907d7e891e650e0e43539811af81f76", + "sampletest_4.bam.bai:md5,786cb1fbbadef4acea403f83d4628d5c", "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463", "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab", @@ -474,7 +772,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638", "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d", - "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,5bdb2f162266ab68005cbfc0a45e311e", + "multiqc_picard_baseContent.txt:md5,409bf8ce546a573ce6678769b84726fd", + "multiqc_picard_quality_by_cycle.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42", + "multiqc_picard_quality_score_distribution.txt:md5,182098ce1ff0a664d873c329d54189df", + "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,ebf56fd9b3b127ff41211e3f79f18b42", + "picard_QualityScoreDistribution_histogram.txt:md5,182098ce1ff0a664d873c329d54189df", + "picard_alignment_readlength_plot.txt:md5,92ab5c6fbe67484da62626736b1b21d4", + "picard_alignment_summary.txt:md5,f54187e8515f9b7c32eabaf1f8702224", + "picard_base_distribution_by_cycle__Adenine.txt:md5,61c7df03f74846ffa484a59fcccc7b9e", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,b4504bbb9ad72796703873f2d957977a", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1d38466783ea51bf0c7be5bceaff4d43", + "picard_base_distribution_by_cycle__Thymine.txt:md5,1b13c9b64042839a3bc65a8553e5ba24", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,75aee7627205c6513389d7a52e7a383b", + "picard_quality_by_cycle.txt:md5,4850a9230f9be5af67f3d934602df440", + "picard_quality_score_distribution.txt:md5,17f8498a5b18cea0eb4796a6e12b8e36", "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994", "fastqc-status-check-heatmap.txt:md5,67afbf7ec626c4fc7a28b4922352bc84", "fastqc_overrepresented_sequences_plot.txt:md5,0356d007eaf807f7b63714b438b11289", @@ -489,7 +804,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff", "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f", - "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,e4cb1b13e6a7298d172ed112a0479b5a", + "multiqc_picard_baseContent.txt:md5,740592a5858706d2b4b8f585a1d5492b", + "multiqc_picard_quality_by_cycle.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5", + "multiqc_picard_quality_score_distribution.txt:md5,59b955203209cfab3d2d21bdfe20997e", + "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,c3f14084aedc511b9f0aa8410e7cb3b5", + "picard_QualityScoreDistribution_histogram.txt:md5,59b955203209cfab3d2d21bdfe20997e", + "picard_alignment_readlength_plot.txt:md5,1f8b2f4df8bd5cf879b96cfb2be6d81c", + "picard_alignment_summary.txt:md5,0cfafd1ed1920270bb1a5d13bed51480", + "picard_base_distribution_by_cycle__Adenine.txt:md5,bd7f8dab8e73406cded6c6f27bbc87e9", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,fe44ccdb08c6955149eacf52a77bbba2", + "picard_base_distribution_by_cycle__Guanine.txt:md5,85a9172769830b4169f214c335f44fdc", + "picard_base_distribution_by_cycle__Thymine.txt:md5,1fe0c42cb22981763862d1934a35de07", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,4c5bfb1594b391f3e36a9e1223b43a94", + "picard_quality_by_cycle.txt:md5,a43e7bb40bc479e9c32476256b09e734", + "picard_quality_score_distribution.txt:md5,a940641c0dab423c964c0f46b69dd805", "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740", "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53", "fastqc_overrepresented_sequences_plot.txt:md5,eac8d0fd31c614d8d0f56bd54ee8c78c", @@ -504,7 +836,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d", "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347", - "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,d4e63eed820edcc71b3e37d793983bd7", + "multiqc_picard_baseContent.txt:md5,0dd5fa539e4034e3539fb1e7068c7ce5", + "multiqc_picard_quality_by_cycle.txt:md5,750eadc27875fc8141b64a90789c369f", + "multiqc_picard_quality_score_distribution.txt:md5,140279eb5abac364c4d4c417105da620", + "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,750eadc27875fc8141b64a90789c369f", + "picard_QualityScoreDistribution_histogram.txt:md5,140279eb5abac364c4d4c417105da620", + "picard_alignment_readlength_plot.txt:md5,a39f6a39dad13dacc2134508dbbf172d", + "picard_alignment_summary.txt:md5,fec83821c097bc1850257ce36aa73e5f", + "picard_base_distribution_by_cycle__Adenine.txt:md5,f206efb4e5344b8cbb2d18f6e73d5d95", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,ebf98e3d0bf661161989bf3d010b8c6b", + "picard_base_distribution_by_cycle__Guanine.txt:md5,f7dff1258977e9d04fb26ba8192facc5", + "picard_base_distribution_by_cycle__Thymine.txt:md5,b32d1e91c41756afe8732107868b32e0", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,b7b249afe807ca2321e6dd839961795c", + "picard_quality_by_cycle.txt:md5,1fe617901a493b80c31fcd01a00c416d", + "picard_quality_score_distribution.txt:md5,5cd4a87942000899776927f22a5db802", "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06", "fastqc-status-check-heatmap.txt:md5,08228a8f3d6f11b174b98626bb22bda1", "fastqc_overrepresented_sequences_plot.txt:md5,3434dfb79f150e2e584e85866983ba01", @@ -519,7 +868,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc", "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78", - "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,22093b80f335c4c53633b01a930157f4", + "multiqc_picard_baseContent.txt:md5,6886e1e5179031ddba4958f301930d64", + "multiqc_picard_quality_by_cycle.txt:md5,96652e2e2d693488df9104e5ae8cb4a7", + "multiqc_picard_quality_score_distribution.txt:md5,879a4470d08fe6d9b1796f46020fb5f5", + "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,96652e2e2d693488df9104e5ae8cb4a7", + "picard_QualityScoreDistribution_histogram.txt:md5,879a4470d08fe6d9b1796f46020fb5f5", + "picard_alignment_readlength_plot.txt:md5,9b323aa8cd934d084e9c83cfa1da306b", + "picard_alignment_summary.txt:md5,4e8970d31940f5e9020851d62e63b2e2", + "picard_base_distribution_by_cycle__Adenine.txt:md5,166a48317764fe7d4b38ed198503fc11", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,8e62c1113b965497e492e17665cdbe97", + "picard_base_distribution_by_cycle__Guanine.txt:md5,fe53f5f9455b928a3edc1661be83592b", + "picard_base_distribution_by_cycle__Thymine.txt:md5,3d069dd67cc0ffc43456c5f3ee427349", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,e371981072ec99d11c6adb5a4034808c", + "picard_quality_by_cycle.txt:md5,0c25ee4cec6842306b28c6a641aa03e1", + "picard_quality_score_distribution.txt:md5,184dcdd53f6aa3b7a0fa2c008d7dc74a", "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d", "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c", "fastqc_overrepresented_sequences_plot.txt:md5,e0b5bfc4b64d37611b51c939e61196fa", @@ -534,23 +900,42 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5", "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5", - "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde", - "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869", - "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6", - "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676", - "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99", - "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3", - "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01", - "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae", - "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b", - "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476", - "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7" + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,edf7faad1da9922fdc692e9cba5cc0c4", + "multiqc_picard_baseContent.txt:md5,9631916c0a9a736811c47ab4c476428f", + "multiqc_picard_quality_by_cycle.txt:md5,9e05b241aabe39232b5182cb59d8edd5", + "multiqc_picard_quality_score_distribution.txt:md5,e9c3ade201964470d2d22569a400fa49", + "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,9e05b241aabe39232b5182cb59d8edd5", + "picard_QualityScoreDistribution_histogram.txt:md5,e9c3ade201964470d2d22569a400fa49", + "picard_alignment_readlength_plot.txt:md5,c2692fde9d899ad61297ad7043fd26b9", + "picard_alignment_summary.txt:md5,5996d5b4c94f16c0efd42e2df47e021e", + "picard_base_distribution_by_cycle__Adenine.txt:md5,a2670974dc96ad8a54f9cc5ae3e09d5e", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,d3b9cc0c99f96814348b57809cf227fb", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1ba086d3fb2676868e8e7b20f55975dc", + "picard_base_distribution_by_cycle__Thymine.txt:md5,8902976984741320fe06004f4115c4f4", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,1380831484d1b069a2fd4a20437118bf", + "picard_quality_by_cycle.txt:md5,b6fc46e18ac875ba02775e7cbf1b8e8b", + "picard_quality_score_distribution.txt:md5,1c17c01ef54a6062a8f1ca8408d32958", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6", + "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a", + "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc", + "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027", + "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775", + "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27", + "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e", + "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d", + "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377", + "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:25:42.576692828" + "timestamp": "2025-11-19T12:19:32.836832601" } } \ No newline at end of file diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap index a539c846..212f45a9 100644 --- a/tests/NovaSeq6000.main_subsample.nf.test.snap +++ b/tests/NovaSeq6000.main_subsample.nf.test.snap @@ -7,7 +7,7 @@ }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", - "samtools": 1.21 + "samtools": "1.22.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -15,8 +15,17 @@ "FASTQSCREEN_FASTQSCREEN": { "fastqscreen": "0.16.0" }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "SAMTOOLS_FAIDX": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.22.1" + }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "SEQTK_SAMPLE": { "seqtk": "1.4-r122" @@ -35,10 +44,15 @@ "bwamem2_index/bwamem2/genome.fa.pac", "bwamem2_mem", "bwamem2_mem/Sample1_1.bam", + "bwamem2_mem/Sample1_1.bam.bai", "bwamem2_mem/Sample23_3.bam", + "bwamem2_mem/Sample23_3.bam.bai", "bwamem2_mem/SampleA_2.bam", + "bwamem2_mem/SampleA_2.bam.bai", "bwamem2_mem/Undetermined_5.bam", + "bwamem2_mem/Undetermined_5.bam.bai", "bwamem2_mem/sampletest_4.bam", + "bwamem2_mem/sampletest_4.bam.bai", "fastqc", "fastqc/Sample1_1_fastqc.html", "fastqc/Sample1_1_fastqc.zip", @@ -89,9 +103,26 @@ "multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt", "multiqc/global_report/multiqc_data/multiqc_fastqc.txt", "multiqc/global_report/multiqc_data/multiqc_general_stats.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_data/multiqc_seqfu.txt", "multiqc/global_report/multiqc_data/multiqc_software_versions.txt", "multiqc/global_report/multiqc_data/multiqc_sources.txt", + "multiqc/global_report/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/global_report/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/global_report/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/global_report/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/global_report/multiqc_data/picard_alignment_summary.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/global_report/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/global_report/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/global_report/multiqc_data/picard_quality_score_distribution.txt", "multiqc/global_report/multiqc_plots", "multiqc/global_report/multiqc_plots/pdf", "multiqc/global_report/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -107,6 +138,16 @@ "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/global_report/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/global_report/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/global_report/multiqc_plots/pdf/seqfu.pdf", "multiqc/global_report/multiqc_plots/png", "multiqc/global_report/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -122,6 +163,16 @@ "multiqc/global_report/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/global_report/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/global_report/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/global_report/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/global_report/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/global_report/multiqc_plots/png/seqfu.png", "multiqc/global_report/multiqc_plots/svg", "multiqc/global_report/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -137,6 +188,16 @@ "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/global_report/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/global_report/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/global_report/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/global_report/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/global_report/multiqc_plots/svg/seqfu.svg", "multiqc/global_report/multiqc_report.html", "multiqc/group_reports", @@ -162,9 +223,26 @@ "multiqc/group_reports/group1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group1/multiqc_plots", "multiqc/group_reports/group1/multiqc_plots/pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -180,6 +258,16 @@ "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group1/multiqc_plots/png", "multiqc/group_reports/group1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -195,6 +283,16 @@ "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group1/multiqc_plots/svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -210,6 +308,16 @@ "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group1/multiqc_report.html", "multiqc/group_reports/group2", @@ -234,9 +342,26 @@ "multiqc/group_reports/group2/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/group2/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/group2/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/group2/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/group2/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/group2/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/group2/multiqc_plots", "multiqc/group_reports/group2/multiqc_plots/pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -252,6 +377,16 @@ "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/group2/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/group2/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/group2/multiqc_plots/png", "multiqc/group_reports/group2/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -267,6 +402,16 @@ "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/group2/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/group2/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/group2/multiqc_plots/png/seqfu.png", "multiqc/group_reports/group2/multiqc_plots/svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -282,6 +427,16 @@ "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/group2/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/group2/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/group2/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/group2/multiqc_report.html", "multiqc/group_reports/lane1", @@ -306,9 +461,26 @@ "multiqc/group_reports/lane1/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/lane1/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/lane1/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/lane1/multiqc_plots", "multiqc/group_reports/lane1/multiqc_plots/pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -324,6 +496,16 @@ "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/lane1/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/lane1/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/lane1/multiqc_plots/png", "multiqc/group_reports/lane1/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -339,6 +521,16 @@ "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/lane1/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/lane1/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/lane1/multiqc_plots/png/seqfu.png", "multiqc/group_reports/lane1/multiqc_plots/svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -354,6 +546,16 @@ "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/lane1/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/lane1/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/lane1/multiqc_report.html", "multiqc/group_reports/test", @@ -378,9 +580,26 @@ "multiqc/group_reports/test/multiqc_data/multiqc_fastq_screen.txt", "multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt", "multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_baseContent.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/multiqc_picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_data/multiqc_seqfu.txt", "multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt", "multiqc/group_reports/test/multiqc_data/multiqc_sources.txt", + "multiqc/group_reports/test/multiqc_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_MeanQualityByCycle_histogram_1.txt", + "multiqc/group_reports/test/multiqc_data/picard_QualityScoreDistribution_histogram.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_readlength_plot.txt", + "multiqc/group_reports/test/multiqc_data/picard_alignment_summary.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Adenine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Cytosine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Guanine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Thymine.txt", + "multiqc/group_reports/test/multiqc_data/picard_base_distribution_by_cycle__Undetermined.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_by_cycle.txt", + "multiqc/group_reports/test/multiqc_data/picard_quality_score_distribution.txt", "multiqc/group_reports/test/multiqc_plots", "multiqc/group_reports/test/multiqc_plots/pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastq_screen_plot-cnt.pdf", @@ -396,6 +615,16 @@ "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_readlength_plot.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-cnt.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_alignment_summary-pct.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_by_cycle.pdf", + "multiqc/group_reports/test/multiqc_plots/pdf/picard_quality_score_distribution.pdf", "multiqc/group_reports/test/multiqc_plots/pdf/seqfu.pdf", "multiqc/group_reports/test/multiqc_plots/png", "multiqc/group_reports/test/multiqc_plots/png/fastq_screen_plot-cnt.png", @@ -411,6 +640,16 @@ "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/group_reports/test/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_readlength_plot.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-cnt.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_alignment_summary-pct.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_by_cycle.png", + "multiqc/group_reports/test/multiqc_plots/png/picard_quality_score_distribution.png", "multiqc/group_reports/test/multiqc_plots/png/seqfu.png", "multiqc/group_reports/test/multiqc_plots/svg", "multiqc/group_reports/test/multiqc_plots/svg/fastq_screen_plot-cnt.svg", @@ -426,10 +665,64 @@ "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/group_reports/test/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_readlength_plot.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-cnt.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_alignment_summary-pct.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_by_cycle.svg", + "multiqc/group_reports/test/multiqc_plots/svg/picard_quality_score_distribution.svg", "multiqc/group_reports/test/multiqc_plots/svg/seqfu.svg", "multiqc/group_reports/test/multiqc_report.html", + "picard_collectmultiplemetrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample1_1.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Sample23_3.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/SampleA_2.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/Undetermined_5.CollectMultipleMetrics.read_length_histogram.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.alignment_summary_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_by_cycle_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution.pdf", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.quality_distribution_metrics", + "picard_collectmultiplemetrics/sampletest_4.CollectMultipleMetrics.read_length_histogram.pdf", "pipeline_info", "pipeline_info/nf_core_seqinspector_software_mqc_versions.yml", + "samtools_faidx", + "samtools_faidx/genome.fa.fai", + "samtools_faidx/genome.fa.sizes", "seqfu_stats", "seqfu_stats/Sample1_1_seqfu.tsv", "seqfu_stats/Sample1_1_seqfu_mqc.txt", @@ -454,11 +747,16 @@ "genome.fa.ann:md5,4439f90bdaaf2cdf9089c9f7f07b9d6b", "genome.fa.bwt.2bit.64:md5,c9a1ea631cf4ad59f4c3549a030c6c5e", "genome.fa.pac:md5,fd24ae5f67c642dfe9453e63350618cc", - "Sample1_1.bam:md5,a948b66ba258785fe12aea5d64136b05", - "Sample23_3.bam:md5,61e745916240193c0ecced45e6a0b054", - "SampleA_2.bam:md5,82a083dcf79d10110a39c736dde463de", - "Undetermined_5.bam:md5,6eb240ce5a28b26c48b72e7d84e976f8", - "sampletest_4.bam:md5,08e4ce7950bb8b0ae9e83b497991b9c9", + "Sample1_1.bam:md5,0bd502d4e221008867c85393cce2b89b", + "Sample1_1.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "Sample23_3.bam:md5,26a49672caec3ab985d3f3dd6bdff530", + "Sample23_3.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "SampleA_2.bam:md5,240d536aab1aac8fa3bca402703121df", + "SampleA_2.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "Undetermined_5.bam:md5,f30b23c562a1725f3f23236acab1fd9a", + "Undetermined_5.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", + "sampletest_4.bam:md5,2c37f72ed4f25c971199fbde3af370b9", + "sampletest_4.bam.bai:md5,20c7b66e8e1ace324a3cbbee6745b714", "Sample1_1_screen.png:md5,562256290643b51e4374c2225a15f463", "Sample1_1_screen.txt:md5,3b184ef10eeb99043a85826534a4ee28", "Sample23_3_screen.png:md5,6bb2caf67b9b2ed25d3d5f32c343e9ab", @@ -483,7 +781,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638", "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514", - "multiqc_seqfu.txt:md5,5b54a49079169985795537d83d58bdd9", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,ae3f9e644215ac39d2eae114bd52a517", + "multiqc_picard_baseContent.txt:md5,8b2efc3fa06d2013348b35f9607292aa", + "multiqc_picard_quality_by_cycle.txt:md5,c2774038d1a0142746426e46f9f954dd", + "multiqc_picard_quality_score_distribution.txt:md5,792755ee794d375b85a57f58d879f0c6", + "multiqc_seqfu.txt:md5,18dd2407d4a1791646785123028f69b5", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,c2774038d1a0142746426e46f9f954dd", + "picard_QualityScoreDistribution_histogram.txt:md5,792755ee794d375b85a57f58d879f0c6", + "picard_alignment_readlength_plot.txt:md5,ebd1ff06394bd202b8190c46d560bc95", + "picard_alignment_summary.txt:md5,e507eccfa0a05b20705f99a3619dde29", + "picard_base_distribution_by_cycle__Adenine.txt:md5,597d0fd368eab8a21cd7f4a92965ecf6", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,ade1d92e5e6d3bfefd3695f103079b6c", + "picard_base_distribution_by_cycle__Guanine.txt:md5,af525e84f95ceb4b8496f734db2420fb", + "picard_base_distribution_by_cycle__Thymine.txt:md5,8b5ada27023f2545792fabbb69a07067", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,a472bba4490d7189df23f6b38a554448", + "picard_quality_by_cycle.txt:md5,83d68b4049173f8c9a37f58f1276adc1", + "picard_quality_score_distribution.txt:md5,42c08c8a51230d9ecccdad416c06f59c", "fastq_screen_plot.txt:md5,c25d34568f10f131156294d31fbfa994", "fastqc-status-check-heatmap.txt:md5,7ee494f345c09706513e65907788de02", "fastqc_overrepresented_sequences_plot.txt:md5,ca9fa146e7b8a7f562fd79b521ba0f60", @@ -498,7 +813,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff", "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab", - "multiqc_seqfu.txt:md5,5579172a6f8ac09a5ffcb3ce6a99590e", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,7bc3f6ef8f47e6f1e060f957025c98aa", + "multiqc_picard_baseContent.txt:md5,1426865fe8ee1a36f67636c28500a91c", + "multiqc_picard_quality_by_cycle.txt:md5,79bf9f861077de70ec28c9af01783876", + "multiqc_picard_quality_score_distribution.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4", + "multiqc_seqfu.txt:md5,6cdb863a3686fbb772aae5a66925ff23", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,79bf9f861077de70ec28c9af01783876", + "picard_QualityScoreDistribution_histogram.txt:md5,a3f8d1937e1f118800aa3d86c1b498c4", + "picard_alignment_readlength_plot.txt:md5,5aed5e7c1395a537bdce7163c93781bd", + "picard_alignment_summary.txt:md5,9d0d003456e08f78701e876d0238b5a6", + "picard_base_distribution_by_cycle__Adenine.txt:md5,73e910febe1ea4d08a9f4e49d6c10615", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,092e732bb44842f2da5416de158c1cc5", + "picard_base_distribution_by_cycle__Guanine.txt:md5,e81495fde738e2954483195fd0ccfb04", + "picard_base_distribution_by_cycle__Thymine.txt:md5,ed9ad958081a904a5584757f87b29eb2", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,2b4526a0b0977ebd7fbe326c6d51cf19", + "picard_quality_by_cycle.txt:md5,d53617c495e81e011996cd4e9f755e0a", + "picard_quality_score_distribution.txt:md5,05f9e89733e43b81acf593efc1a56180", "fastq_screen_plot.txt:md5,44fca6453b0a3d0590271bd7a31cc740", "fastqc-status-check-heatmap.txt:md5,b6872d9dbaa3cce396d48dc137076e53", "fastqc_overrepresented_sequences_plot.txt:md5,19babef6996c0bfdf28e5df89368cbb1", @@ -513,7 +845,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d", "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b", - "multiqc_seqfu.txt:md5,b5434520fa5be5c98be5ed164a464d23", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,4dc89e1a04843d44695ecc8d1f047ee8", + "multiqc_picard_baseContent.txt:md5,0a5f9d32dd3061ce4349518c47d69838", + "multiqc_picard_quality_by_cycle.txt:md5,ec59b472afc1242ff299011ba456e792", + "multiqc_picard_quality_score_distribution.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf", + "multiqc_seqfu.txt:md5,f821357507fda2d4cfd9299f52fa7dc1", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,ec59b472afc1242ff299011ba456e792", + "picard_QualityScoreDistribution_histogram.txt:md5,1b8be76b60ee71aa36a98d34e433b9bf", + "picard_alignment_readlength_plot.txt:md5,72e0094fcd2546bee02a7ac65a3ea218", + "picard_alignment_summary.txt:md5,19586495e6d7904a2a4a7eb9ba17a412", + "picard_base_distribution_by_cycle__Adenine.txt:md5,a825de2b668791e58f6a4078e0b31483", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,59633faead8aa9027883481b0c7e22af", + "picard_base_distribution_by_cycle__Guanine.txt:md5,f02153a346f7e24f200bf06af2293352", + "picard_base_distribution_by_cycle__Thymine.txt:md5,0725af81caa647ec22050c573dfe8cb0", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,3536e6dcc7c7ed972b02d2945da75cb7", + "picard_quality_by_cycle.txt:md5,be127a96dd68c14077548d36c0507dc3", + "picard_quality_score_distribution.txt:md5,9e27b097f10cb9a9a95a3445b220d104", "fastq_screen_plot.txt:md5,5f748d33a7a396547fe8c260b728aa06", "fastqc-status-check-heatmap.txt:md5,bab59a0bd1d676d90cdd986fbba36b26", "fastqc_overrepresented_sequences_plot.txt:md5,79cb259874c52b44f8c69b2075ee498e", @@ -528,7 +877,24 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc", "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8", - "multiqc_seqfu.txt:md5,e2e092852c011abe5ad75cdcd68b9383", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,fa26e8b96faa1926d8f41fc3fe959ff7", + "multiqc_picard_baseContent.txt:md5,b9d72d8173cdc7649b44b80aa485477c", + "multiqc_picard_quality_by_cycle.txt:md5,062547fb888ed508dd1d5733d7bed22e", + "multiqc_picard_quality_score_distribution.txt:md5,dd5abab3a7141654fffa3946c50a039b", + "multiqc_seqfu.txt:md5,8cced36d66ca9d25d60c006e734aa7e9", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,062547fb888ed508dd1d5733d7bed22e", + "picard_QualityScoreDistribution_histogram.txt:md5,dd5abab3a7141654fffa3946c50a039b", + "picard_alignment_readlength_plot.txt:md5,e5d397c216a0911a73dff5550fa7b1d7", + "picard_alignment_summary.txt:md5,ef16e8dbab178f44deebe0f4d321097b", + "picard_base_distribution_by_cycle__Adenine.txt:md5,8ada743b028ec78996f9dc40f1922941", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,c97859ee1641de9bff58dbd1e82fff20", + "picard_base_distribution_by_cycle__Guanine.txt:md5,ea86115ef2ca4ff4922486ceb6c6e1e8", + "picard_base_distribution_by_cycle__Thymine.txt:md5,07a3f1e6b1ed2bc55128fc2a0f46eb92", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,67ee93606c468a7eea7818b2f4b3389f", + "picard_quality_by_cycle.txt:md5,974b3baed160e9643f493df1d0ad5000", + "picard_quality_score_distribution.txt:md5,869d69ae4e243f0669f63b489563e4f1", "fastq_screen_plot.txt:md5,8622e1dbd0fe62520af6096207b9775d", "fastqc-status-check-heatmap.txt:md5,2a66f5d61b9eb579555905cd5954b04c", "fastqc_overrepresented_sequences_plot.txt:md5,5cdefa954db6e46c286e2984a883eb18", @@ -543,17 +909,36 @@ "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a", "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5", "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f", - "multiqc_seqfu.txt:md5,a1a0b9a0dde0c1c4fe184d44c675dcde", - "Sample1_1_seqfu.tsv:md5,269fabf8435defcd327aa69a050b7869", - "Sample1_1_seqfu_mqc.txt:md5,a354b0ed16b9cf84aa88f501d7740fd6", - "Sample23_3_seqfu.tsv:md5,6fdadbeeefccbf957f880d6852bf9676", - "Sample23_3_seqfu_mqc.txt:md5,e94269e3efc8b8192d7ac9c15ea2aa99", - "SampleA_2_seqfu.tsv:md5,b980ed694a05825fcf7c8b5b73888eb3", - "SampleA_2_seqfu_mqc.txt:md5,1d4b0e918644cf553108b7ccf77b4a01", - "Undetermined_5_seqfu.tsv:md5,b4458d41df4dee9321da03f4d4672aae", - "Undetermined_5_seqfu_mqc.txt:md5,0c869488cb61d2f87758c621bded212b", - "sampletest_4_seqfu.tsv:md5,db3179b0c41a09e6317a5a5c0852f476", - "sampletest_4_seqfu_mqc.txt:md5,590b97cc48268629204f59007bae7ad7", + "multiqc_picard_AlignmentSummaryMetrics.txt:md5,55627d8016b72c37c104e03cc156862c", + "multiqc_picard_baseContent.txt:md5,974d83faa49711ab4ea1248c59e69393", + "multiqc_picard_quality_by_cycle.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba", + "multiqc_picard_quality_score_distribution.txt:md5,5e7e80654e12c500b15f8564ffb12b27", + "multiqc_seqfu.txt:md5,ff4ce1c88f39ed24a88bae0a861f75c8", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram_1.txt:md5,248ecaf269d8fef1e84ea06f98b6f6ba", + "picard_QualityScoreDistribution_histogram.txt:md5,5e7e80654e12c500b15f8564ffb12b27", + "picard_alignment_readlength_plot.txt:md5,23ff551a5a8eded1857356f38b19039c", + "picard_alignment_summary.txt:md5,c741b69e17ed84370732b567ae11c69c", + "picard_base_distribution_by_cycle__Adenine.txt:md5,fc37dd1ac805881a467b264a7dd76677", + "picard_base_distribution_by_cycle__Cytosine.txt:md5,7993fd56aa542b71bc984cd36c489fd1", + "picard_base_distribution_by_cycle__Guanine.txt:md5,1bca639db2a2624727f7b6dd2aa1442e", + "picard_base_distribution_by_cycle__Thymine.txt:md5,a5f0903d77b6060676f7dda249b99738", + "picard_base_distribution_by_cycle__Undetermined.txt:md5,102e653a543ac908ac9ec9b86412d73b", + "picard_quality_by_cycle.txt:md5,3d43fd5387c0dc728833c681ea4f73cc", + "picard_quality_score_distribution.txt:md5,9d9f1bb12316175cdb88d3ff70305428", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "Sample1_1_seqfu.tsv:md5,ac174f48d928c6ddfd43c88af0caa8b6", + "Sample1_1_seqfu_mqc.txt:md5,24d99524ccd0e6c6255a69d68a871c7a", + "Sample23_3_seqfu.tsv:md5,6fac5d3dbce3f3bee72341fe99a399dc", + "Sample23_3_seqfu_mqc.txt:md5,4d4f280911a08bb6b753142980178027", + "SampleA_2_seqfu.tsv:md5,aec811f267bb2a0ef066a7abb59d2775", + "SampleA_2_seqfu_mqc.txt:md5,a819409a5cb64e20c3e54ec5ada4aa27", + "Undetermined_5_seqfu.tsv:md5,3a42c5c66a0a118f1a6f6f6e560b0e7e", + "Undetermined_5_seqfu_mqc.txt:md5,bd8be908362c5cb08a72f8ae7ab41b0d", + "sampletest_4_seqfu.tsv:md5,a5bea0b9c6015dd1a201ffd433e9b377", + "sampletest_4_seqfu_mqc.txt:md5,2180961655bbc8a12f0152d6a4b803a2", "Sample1_1_Sample1_S1_L001_R1_001.fastq.gz:md5,3ccd132ff32399706842b0f1d00f477e", "Sample23_3_Sample23_S3_L001_R1_001.fastq.gz:md5,3802f03450693b42531fdf5b0b542c2f", "SampleA_2_SampleA_S2_L001_R1_001.fastq.gz:md5,f99d5407aac64cb36451c6f0a1db5ade", @@ -565,6 +950,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:26:40.559862265" + "timestamp": "2025-11-19T12:20:48.844054564" } } \ No newline at end of file diff --git a/tests/PromethION.main.nf.test.config b/tests/PromethION.main.nf.test.config index 526df7be..46e9c091 100644 --- a/tests/PromethION.main.nf.test.config +++ b/tests/PromethION.main.nf.test.config @@ -6,4 +6,5 @@ params { input = params.pipelines_testdata_base_path + 'seqinspector/testdata/PromethION/samplesheet.csv' genome = 'EB1' skip_tools = 'bwamem2_index,bwamem2_mem' + } diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap index 0467b847..be8a9183 100644 --- a/tests/PromethION.main.nf.test.snap +++ b/tests/PromethION.main.nf.test.snap @@ -9,7 +9,7 @@ "fastqscreen": "0.16.0" }, "SEQFU_STATS": { - "seqfu": "1.20.3" + "seqfu": "1.22.3" }, "Workflow": { "nf-core/seqinspector": "v1.0dev" @@ -126,13 +126,13 @@ "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0", "multiqc_seqfu.txt:md5,9595d608ff5709f2bdec8cb1016416c0", "hg001_1_seqfu.tsv:md5,b133752c897afbb4d8721b911fa117d4", - "hg001_1_seqfu_mqc.txt:md5,6285f582c03faa70e8dcb3503e5db728" + "hg001_1_seqfu_mqc.txt:md5,42e3506b02ceb72a6f05cb174505e722" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-07T10:27:14.736749139" + "timestamp": "2025-11-19T12:21:24.011932536" } } \ No newline at end of file diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf index 5aaa34fa..3e7b25cd 100644 --- a/workflows/seqinspector.nf +++ b/workflows/seqinspector.nf @@ -12,7 +12,9 @@ include { SEQFU_STATS } from '../modules/nf-core/seqfu/stats' include { FASTQSCREEN_FASTQSCREEN } from '../modules/nf-core/fastqscreen/fastqscreen/main' include { BWAMEM2_INDEX } from '../modules/nf-core/bwamem2/index/main' include { BWAMEM2_MEM } from '../modules/nf-core/bwamem2/mem/main' - +include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' +include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx/main' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../modules/nf-core/picard/collectmultiplemetrics/main' include { MULTIQC as MULTIQC_GLOBAL } from '../modules/nf-core/multiqc/main' include { MULTIQC as MULTIQC_PER_TAG } from '../modules/nf-core/multiqc/main' @@ -40,6 +42,13 @@ workflow SEQINSPECTOR { ch_multiqc_extra_files = Channel.empty() ch_multiqc_reports = Channel.empty() +// Initialize all channels that might be used later + ch_bwamem2_index = Channel.empty() + ch_bwamem2_mem = Channel.empty() + ch_samtools_index = Channel.empty() + ch_reference_fasta_fai = Channel.empty() + ch_reference_fasta = Channel.empty() + // // MODULE: Run Seqtk sample to perform subsampling // @@ -133,6 +142,53 @@ workflow SEQINSPECTOR { } + // MODULE: Index BAM files with Samtools + if (!("samtools_index" in skip_tools) && !("bwamem2_mem" in skip_tools)) { + SAMTOOLS_INDEX ( + ch_bwamem2_mem + ) + ch_samtools_index = SAMTOOLS_INDEX.out.bai + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + } + + // MODULE: Index reference FASTA with Samtools faidx + if (!("samtools_faidx" in skip_tools)) { + + // Assume ch_fasta emits tuple(meta, fasta) + SAMTOOLS_FAIDX ( + ch_reference_fasta, + [[:],[]], + true // get_sizes + ) + ch_reference_fasta_fai = SAMTOOLS_FAIDX.out.fai + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + } + + // MODULE: Prepare BAM/BAI tuples for Picard + // Combine BAM and BAI outputs for Picard + if (!("picard_collectmultiplemetrics" in skip_tools) && + !("bwamem2_mem" in skip_tools) && + !("samtools_index" in skip_tools) && + !("samtools_faidx" in skip_tools)) { + + // Prepare BAM/BAI tuples for Picard + ch_bam_bai = ch_bwamem2_mem + .join(ch_samtools_index, failOnDuplicate: true, failOnMismatch: true) + + ch_fasta = ch_reference_fasta + ch_fai = ch_reference_fasta_fai + + + PICARD_COLLECTMULTIPLEMETRICS( + ch_bam_bai, + ch_fasta, + ch_fai + ) + + ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTMULTIPLEMETRICS.out.metrics) + ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) + } + // Collate and save software versions //