From 8ed74a4801e29dbac482d6dc287a5230c8f17216 Mon Sep 17 00:00:00 2001 From: chaochaowong Date: Fri, 28 Nov 2025 09:15:59 -0800 Subject: [PATCH 1/3] update hiphase verstion to 1.5.0 --- modules/nf-core/hiphase/environment.yml | 2 +- modules/nf-core/hiphase/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/hiphase/environment.yml b/modules/nf-core/hiphase/environment.yml index f0ee56e0472a..927a235dc3ce 100644 --- a/modules/nf-core/hiphase/environment.yml +++ b/modules/nf-core/hiphase/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hiphase=1.4.5 + - bioconda::hiphase=1.5.0 diff --git a/modules/nf-core/hiphase/main.nf b/modules/nf-core/hiphase/main.nf index 46b104e2feb5..b4a2c3586a1a 100644 --- a/modules/nf-core/hiphase/main.nf +++ b/modules/nf-core/hiphase/main.nf @@ -4,8 +4,8 @@ process HIPHASE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hiphase:1.4.5--h9ee0642_0': - 'biocontainers/hiphase:1.4.5--h9ee0642_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d4/d418cdbaff565e9c563c441c72d480f2605bb529712dd026068f1d0a7b246617/data': + 'community.wave.seqera.io/library/hiphase:1.5.0--f36e5874e9287052' }" input: tuple val(meta), path(vcf), path(csi) From c8c15b4404d3f07eeb47d89b595160eb036d404a Mon Sep 17 00:00:00 2001 From: chaochaowong Date: Fri, 28 Nov 2025 09:30:31 -0800 Subject: [PATCH 2/3] add the *.phased.bam as an output file --- modules/nf-core/hiphase/main.nf | 4 +++- modules/nf-core/hiphase/meta.yml | 17 ++++++++++++++--- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/hiphase/main.nf b/modules/nf-core/hiphase/main.nf index b4a2c3586a1a..e07b7f6ef3c6 100644 --- a/modules/nf-core/hiphase/main.nf +++ b/modules/nf-core/hiphase/main.nf @@ -8,11 +8,12 @@ process HIPHASE { 'community.wave.seqera.io/library/hiphase:1.5.0--f36e5874e9287052' }" input: - tuple val(meta), path(vcf), path(csi) + tuple val(meta) , path(vcf), path(csi) tuple val(meta2), path(bam), path(bai) tuple val(meta3), path(fasta) output: + tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.vcf"), emit: vcf tuple val(meta), path("*.csv"), emit: csv path "versions.yml" , emit: versions @@ -44,6 +45,7 @@ process HIPHASE { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ + touch ${prefix}.phased.bam touch ${prefix}.phased.vcf touch ${prefix}.stats.csv diff --git a/modules/nf-core/hiphase/meta.yml b/modules/nf-core/hiphase/meta.yml index d8f75ec2d2cc..10611d033e05 100644 --- a/modules/nf-core/hiphase/meta.yml +++ b/modules/nf-core/hiphase/meta.yml @@ -56,6 +56,18 @@ input: pattern: "*.{fasta}" ontologies: [] output: + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Phased BAM file with haplotag information + pattern: "*.bam" + ontologies: + - edam: http://edamontology.org/format_2572 # BAM vcf: - - meta: type: map @@ -66,7 +78,8 @@ output: type: file description: Phased VCF file pattern: "*.vcf" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_3016 # VCF csv: - - meta: type: map @@ -77,7 +90,6 @@ output: type: file description: stats associated with the phasing pattern: "*.csv" - ontologies: - edam: http://edamontology.org/format_3752 # CSV versions: @@ -85,7 +97,6 @@ output: type: file description: File containing software versions pattern: "versions.yml" - ontologies: - edam: http://edamontology.org/format_3750 # YAML authors: From 3b642379a1e04ee7683d0d6dd28a7f185dab2a84 Mon Sep 17 00:00:00 2001 From: chaochaowong Date: Fri, 28 Nov 2025 09:38:20 -0800 Subject: [PATCH 3/3] update test snapshot --- .../nf-core/hiphase/tests/main.nf.test.snap | 62 ++++++++++++++----- 1 file changed, 47 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/hiphase/tests/main.nf.test.snap b/modules/nf-core/hiphase/tests/main.nf.test.snap index fe2c269e3dbc..e4dbdccb868e 100644 --- a/modules/nf-core/hiphase/tests/main.nf.test.snap +++ b/modules/nf-core/hiphase/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.phased.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.phased.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -15,11 +15,27 @@ { "id": "test" }, - "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.phased.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ - "versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7" + [ + { + "id": "test" + }, + "test.stats.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.phased.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "csv": [ [ @@ -38,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7" + "versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96" ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.7" }, - "timestamp": "2024-10-25T15:30:16.272259201" + "timestamp": "2025-11-28T09:37:10.934639568" }, "homo_sapiens pacbio [vcf] [csi] [bam] [bai] [fasta]": { "content": [ @@ -56,7 +72,7 @@ { "id": "test" }, - "test.phased.vcf:md5,8d27a1ef3c4b28662a7559ea2ccc4681" + "test.phased.bam:md5,ea563e2c998cabc656f3fead4161f6d8" ] ], "1": [ @@ -64,11 +80,27 @@ { "id": "test" }, - "test.stats.csv:md5,9901e909f6898db2b2a9d083a4f478d5" + "test.phased.vcf:md5,c4b24d778e57a1cc809de984c8bf9361" ] ], "2": [ - "versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7" + [ + { + "id": "test" + }, + "test.stats.csv:md5,9901e909f6898db2b2a9d083a4f478d5" + ] + ], + "3": [ + "versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.phased.bam:md5,ea563e2c998cabc656f3fead4161f6d8" + ] ], "csv": [ [ @@ -83,18 +115,18 @@ { "id": "test" }, - "test.phased.vcf:md5,8d27a1ef3c4b28662a7559ea2ccc4681" + "test.phased.vcf:md5,c4b24d778e57a1cc809de984c8bf9361" ] ], "versions": [ - "versions.yml:md5,bdbe594b7912bdb1acefa03993d4ddf7" + "versions.yml:md5,d575d9f2bec6c1c5c4206b80ba7dfc96" ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.7" }, - "timestamp": "2024-11-06T12:46:36.677573258" + "timestamp": "2025-11-28T09:37:04.541231653" } } \ No newline at end of file