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Merged
CharlotteAnne merged 29 commits into from
Dec 19, 2024
Merged

merge latest version to master 1.2 #31

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25f75d0
Merge branch 'master' into dev
CharlotteAnne Nov 13, 2023
0ac42c2
allow multimapping genome output bams
CharlotteAnne Nov 13, 2023
7654544
publish bowtie premapping bam
CharlotteAnne Nov 14, 2023
46a1203
dedup multi bam and smrna bam
CharlotteAnne Nov 14, 2023
a99fc3c
Update schema
chris-cheshire Nov 16, 2023
8b0aa7c
Merge branch 'dev' of https://github.com/goodwright/clipseq into dev
chris-cheshire Nov 16, 2023
c357a3a
add trna/rrna premap count to icount_summary output
CharlotteAnne Nov 28, 2023
833605b
Merge remote-tracking branch 'origin/dev' into dev
CharlotteAnne Nov 28, 2023
614e725
expose all trim galore args
CharlotteAnne Nov 28, 2023
fcb224e
tidy up the output folders
CharlotteAnne Nov 28, 2023
f49ba74
update flow schema
CharlotteAnne Nov 28, 2023
de15a01
get rid of min trim from schema, doesnt exist anymore
CharlotteAnne Nov 28, 2023
6d3cd67
test for icount summary publishing
CharlotteAnne Nov 28, 2023
bf7db75
use samtools to sort multimapped genome bam instead of star
CharlotteAnne Nov 30, 2023
1d0aa3a
avoid UMICOLLAPSE Error: java.lang.StackOverflowError
slbai01 Feb 29, 2024
591e8fb
avoid samtools Error: Argument list too long
slbai01 Feb 29, 2024
82203b4
Fix filename absolute references
slbai01 Feb 29, 2024
720a90a
update peka outputs
CharlotteAnne Apr 10, 2024
b419cd8
Merge pull request #27 from slbai01/patch-1
CharlotteAnne Apr 23, 2024
653b345
revert changes on samtools simple view
CharlotteAnne Apr 24, 2024
461acb7
update umicollapse
CharlotteAnne Apr 26, 2024
84e81e3
Update main.nf
CharlotteAnne Apr 26, 2024
8837d1e
Update main.nf
CharlotteAnne Apr 26, 2024
3f9b9fc
Update main.nf
CharlotteAnne Apr 26, 2024
0974a3d
Merge branch '1.1' into dev
CharlotteAnne Apr 29, 2024
35f883a
update to using nf-core umicollapse module
CharlotteAnne Apr 29, 2024
1148dc6
1.2 clipseq.json upgrade
samirelanduk Dec 2, 2024
94cf9a0
1.2 prepare_genome.json upgrade
samirelanduk Dec 2, 2024
1422da5
Merge branch 'master' into 1.2
CharlotteAnne Dec 19, 2024
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178 changes: 164 additions & 14 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ if(params.run_trim_galore_fastqc && !params.skip_fastqc) {
if(params.run_trim_galore_fastqc && !params.skip_trimming) {
process {
withName: 'CLIPSEQ:FASTQC_TRIMGALORE:TRIMGALORE' {
ext.args = "--fastqc --length ${params.trim_length} -q 20"
ext.args = "${params.trimgalore_params}"
publishDir = [
[
path: { "${params.outdir}/01_prealign/post_trim_fastqc" },
Expand Down Expand Up @@ -279,6 +279,31 @@ if(params.run_alignment) {
]
}

withName: 'CLIPSEQ:RNA_ALIGN:BOWTIE_ALIGN_K1' {
ext.args = { "-v 2 -m 100 --norc --best --strata -k 1" }
ext.prefix = { "${meta.id}_withK1" }
publishDir = [
[
path: { "${params.outdir}/02_alignment/smrna" },
mode: "${params.publish_dir_mode}",
pattern: '*.out',
enabled: true
],
[
path: { "${params.outdir}/02_alignment/smrna" },
mode: "${params.publish_dir_mode}",
pattern: '*.bam',
enabled: false
],
[
path: { "${params.outdir}/02_alignment/smrna/unmapped" },
mode: "${params.publish_dir_mode}",
pattern: '*.fastq.gz',
enabled: false
]
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_SORT_SMRNA' {
ext.prefix = { "${meta.id}_sorted" }
publishDir = [
Expand All @@ -297,9 +322,22 @@ if(params.run_alignment) {
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_SORT_SMRNA_K1' {
publishDir = [
enabled: false
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_INDEX_SMRNA_K1' {
publishDir = [
enabled: false
]
}


withName: 'CLIPSEQ:RNA_ALIGN:STAR_ALIGN' {
ext.args = { "--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM ${params.star_params}" }
ext.args = { "--readFilesCommand zcat --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM ${params.star_params}" }
ext.prefix = { "${meta.id}_multi" }
publishDir = [
[
path: { "${params.outdir}/02_alignment/genome/log" },
Expand All @@ -321,16 +359,24 @@ if(params.run_alignment) {
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_INDEX_GENOME' {
withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_INDEX_TRANSCRIPT' {
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
enabled: params.save_align_intermed
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_INDEX_TRANSCRIPT' {
ext.prefix = { "${meta.id}_Aligned.toTranscriptome_sorted.out" }
withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_SORT_GENOME' {
ext.prefix = { "${meta.id}_multi.Aligned.toGenome_sorted.out" }
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
enabled: params.save_align_intermed
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_INDEX_GENOME' {
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
Expand All @@ -339,15 +385,35 @@ if(params.run_alignment) {
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_SORT_TRANSCRIPT' {
ext.prefix = { "${meta.id}_Aligned.toTranscriptome_sorted.out" }
ext.prefix = { "${meta.id}_multi.Aligned.toTranscriptome_sorted.out" }
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
enabled: params.save_align_intermed
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_VIEW_GENOME' {
ext.prefix = { "${meta.id}_unique_genome" }
ext.args = "-q 5 --output-fmt bam --write-index"
ext.index_type = "bai"
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
enabled: params.save_align_intermed
]
}

withName: 'CLIPSEQ:RNA_ALIGN:SAMTOOLS_VIEW_TRANSCRIPT' {
ext.prefix = { "${meta.id}_unique_transcriptome" }
ext.args = "-q 5 --output-fmt bam --write-index"
ext.index_type = "bai"
publishDir = [
path: { "${params.outdir}/02_alignment/genome" },
mode: "${params.publish_dir_mode}",
enabled: params.save_align_intermed
]
}
}
}

Expand Down Expand Up @@ -393,30 +459,75 @@ if(params.run_read_filter) {

if(params.run_umi_dedup) {
process {
withName: 'CLIPSEQ:GENOME_DEDUP:UMICOLLAPSE' {
withName: 'CLIPSEQ:GENOME_UNIQUE_DEDUP:UMICOLLAPSE' {
ext.args = { "--umi-sep ${params.umi_separator}" }
ext.prefix = { "${meta.id}.genome.dedup" }
ext.prefix = { "${meta.id}.unique_genome.dedup" }
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:GENOME_DEDUP:SAMTOOLS_INDEX' {
withName: 'CLIPSEQ:GENOME_MULTI_DEDUP:UMICOLLAPSE' {
ext.args = { "--umi-sep ${params.umi_separator}" }
ext.prefix = { "${meta.id}.multi_genome.dedup" }
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:GENOME_DEDUP:BAM_STATS_SAMTOOLS:.*' {
ext.prefix = { "${meta.id}.genome.dedup" }
withName: 'CLIPSEQ:SMRNA_DEDUP:UMICOLLAPSE' {
ext.args = { "--umi-sep ${params.umi_separator}" }
ext.prefix = { "${meta.id}.smrna.dedup" }
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
pattern: "*.{stats,flagstat,idxstats}"
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:SMRNA_K1_DEDUP:UMICOLLAPSE' {
ext.args = { "--umi-sep ${params.umi_separator}" }
ext.prefix = { "${meta.id}.smrna_withk1.dedup" }
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:GENOME_UNIQUE_DEDUP:SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:GENOME_MULTI_DEDUP:SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:SMRNA_DEDUP:SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:SMRNA_K1_DEDUP:SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/03_filt_dedup" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

Expand Down Expand Up @@ -569,6 +680,37 @@ if(params.run_calc_crosslinks) {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
withName: 'CLIPSEQ:CALC_SMRNA_K1_CROSSLINKS:MERGE_AND_SORT' {
ext.cmd1 = 'sort -k1,1 -k2,2n'
ext.suffix = '.smrna_withk1'
ext.ext = 'bed'
publishDir = [
path: { "${params.outdir}/04_crosslinks" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:CALC_SMRNA_K1_CROSSLINKS:CROSSLINK_COVERAGE' {
ext.cmd1 = 'awk \'{OFS = "\t"}{if (\$6 == "+") {print \$1, \$2, \$3, \$5} else {print \$1, \$2, \$3, -\$5}}\' | sort -k1,1 -k2,2n'
ext.suffix = '.smrna_withk1'
ext.ext = 'bedgraph'
publishDir = [
path: { "${params.outdir}/04_crosslinks" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CLIPSEQ:CALC_SMRNA_K1_CROSSLINKS:CROSSLINK_NORMCOVERAGE' {
ext.cmd1 = 'awk -v total=\$CMD2 \'{printf "%s\\t%i\\t%i\\t%s\\t%f\\t%s\\n", \$1, \$2, \$3, \$4, 1000000*\$5/total, \$6}\' | awk \'{OFS = "\t"}{if (\$6 == "+") {print \$1, \$2, \$3, \$5} else {print \$1, \$2, \$3, -\$5}}\' | sort -k1,1 -k2,2n'
ext.cmd2 = 'awk \'BEGIN {total=0} {total=total+\$5} END {print total}\''
ext.suffix = '.norm.smrna_withk1'
ext.ext = 'bedgraph'
publishDir = [
enabled: false
]
}
}
}

Expand Down Expand Up @@ -670,8 +812,13 @@ if(params.run_peak_calling) {
]
}


withName: 'CLIPSEQ:ICOUNT_ANALYSE:ICOUNT_SUMMARY' {
publishDir = [
enabled: false
]
}

withName: 'CLIPSEQ:ICOUNT_ANALYSE:MERGE_SUMMARY' {
publishDir = [
path: { "${params.outdir}/05_peak_calling/icount" },
mode: "${params.publish_dir_mode}",
Expand All @@ -689,7 +836,10 @@ if(params.run_peak_calling) {

withName: 'CLIPSEQ:ICOUNT_ANALYSE:ICOUNT_SIGXLS' {
publishDir = [
enabled: false
path: { "${params.outdir}/05_peak_calling/icount" },
mode: "${params.publish_dir_mode}",
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
pattern: "*.scores.tsv"
]
}

Expand Down
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