From ef943522caf8c483d5f121a358ec629953c83689 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 14 Oct 2019 18:15:18 +0200
Subject: [PATCH] indent main
---
main.nf | 388 ++++++++++++++++++++++++++++----------------------------
1 file changed, 193 insertions(+), 195 deletions(-)
diff --git a/main.nf b/main.nf
index 94c7ae0..697c12c 100644
--- a/main.nf
+++ b/main.nf
@@ -405,36 +405,36 @@ process bowtie2_end_to_end {
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
input:
- set val(sample), file(reads) from raw_reads
- file index from bwt2_index_end2end.collect()
+ set val(sample), file(reads) from raw_reads
+ file index from bwt2_index_end2end.collect()
output:
- set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end
- set val(prefix), file("${prefix}.bam") into end_to_end_bam
+ set val(prefix), file("${prefix}_unmap.fastq") into unmapped_end_to_end
+ set val(prefix), file("${prefix}.bam") into end_to_end_bam
script:
- prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
- def bwt2_opts = params.bwt2_opts_end2end
-
- if (!params.dnase){
- """
- bowtie2 --rg-id BMG --rg SM:${prefix} \\
- ${bwt2_opts} \\
- -p ${task.cpus} \\
- -x ${index}/${bwt2_base} \\
- --un ${prefix}_unmap.fastq \\
- -U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
- """
- }else{
- """
- bowtie2 --rg-id BMG --rg SM:${prefix} \\
- ${bwt2_opts} \\
- -p ${task.cpus} \\
- -x ${index}/${bwt2_base} \\
- --un ${prefix}_unmap.fastq \\
- -U ${reads} > ${prefix}.bam
- """
- }
+ prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
+ def bwt2_opts = params.bwt2_opts_end2end
+
+ if (!params.dnase){
+ """
+ bowtie2 --rg-id BMG --rg SM:${prefix} \\
+ ${bwt2_opts} \\
+ -p ${task.cpus} \\
+ -x ${index}/${bwt2_base} \\
+ --un ${prefix}_unmap.fastq \\
+ -U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
+ """
+ }else{
+ """
+ bowtie2 --rg-id BMG --rg SM:${prefix} \\
+ ${bwt2_opts} \\
+ -p ${task.cpus} \\
+ -x ${index}/${bwt2_base} \\
+ --un ${prefix}_unmap.fastq \\
+ -U ${reads} > ${prefix}.bam
+ """
+ }
}
process trim_reads {
@@ -443,20 +443,20 @@ process trim_reads {
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
when:
- !params.dnase
+ !params.dnase
input:
- set val(prefix), file(reads) from unmapped_end_to_end
+ set val(prefix), file(reads) from unmapped_end_to_end
output:
- set val(prefix), file("${prefix}_trimmed.fastq") into trimmed_reads
+ set val(prefix), file("${prefix}_trimmed.fastq") into trimmed_reads
script:
- """
- cutsite_trimming --fastq $reads \\
- --cutsite ${params.ligation_site} \\
- --out ${prefix}_trimmed.fastq
- """
+ """
+ cutsite_trimming --fastq $reads \\
+ --cutsite ${params.ligation_site} \\
+ --out ${prefix}_trimmed.fastq
+ """
}
process bowtie2_on_trimmed_reads {
@@ -465,24 +465,24 @@ process bowtie2_on_trimmed_reads {
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
when:
- !params.dnase
+ !params.dnase
input:
- set val(prefix), file(reads) from trimmed_reads
- file index from bwt2_index_trim.collect()
+ set val(prefix), file(reads) from trimmed_reads
+ file index from bwt2_index_trim.collect()
output:
- set val(prefix), file("${prefix}_trimmed.bam") into trimmed_bam
+ set val(prefix), file("${prefix}_trimmed.bam") into trimmed_bam
script:
- prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
- """
- bowtie2 --rg-id BMG --rg SM:${prefix} \\
- ${params.bwt2_opts_trimmed} \\
- -p ${task.cpus} \\
- -x ${index}/${bwt2_base} \\
- -U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
- """
+ prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
+ """
+ bowtie2 --rg-id BMG --rg SM:${prefix} \\
+ ${params.bwt2_opts_trimmed} \\
+ -p ${task.cpus} \\
+ -x ${index}/${bwt2_base} \\
+ -U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
+ """
}
if (!params.dnase){
@@ -492,39 +492,39 @@ if (!params.dnase){
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
input:
- set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam )
+ set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam )
output:
- set val(sample), file("${prefix}_bwt2merged.bam") into bwt2_merged_bam
- set val(oname), file("${prefix}.mapstat") into all_mapstat
+ set val(sample), file("${prefix}_bwt2merged.bam") into bwt2_merged_bam
+ set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
- sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
- tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
- oname = prefix.toString() - ~/(\.[0-9]+)$/
+ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
+ tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
+ oname = prefix.toString() - ~/(\.[0-9]+)$/
- """
- samtools merge -@ ${task.cpus} \\
- -f ${prefix}_bwt2merged.bam \\
- ${bam1} ${bam2}
+ """
+ samtools merge -@ ${task.cpus} \\
+ -f ${prefix}_bwt2merged.bam \\
+ ${bam1} ${bam2}
- samtools sort -@ ${task.cpus} -m 800M \\
+ samtools sort -@ ${task.cpus} -m 800M \\
-n -T /tmp/ \\
-o ${prefix}_bwt2merged.sorted.bam \\
${prefix}_bwt2merged.bam
- mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
-
- echo "## ${prefix}" > ${prefix}.mapstat
- echo -n "total_${tag}\t" >> ${prefix}.mapstat
- samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
- echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
- samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
- echo -n "global_${tag}\t" >> ${prefix}.mapstat
- samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
- echo -n "local_${tag}\t" >> ${prefix}.mapstat
- samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
- """
+ mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
+
+ echo "## ${prefix}" > ${prefix}.mapstat
+ echo -n "total_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+ echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+ echo -n "global_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+ echo -n "local_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
+ """
}
}else{
process dnase_mapping_stats{
@@ -533,27 +533,27 @@ if (!params.dnase){
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
input:
- set val(prefix), file(bam1) from end_to_end_bam
+ set val(prefix), file(bam1) from end_to_end_bam
output:
- set val(sample), file(bam1) into bwt2_merged_bam
- set val(oname), file("${prefix}.mapstat") into all_mapstat
+ set val(sample), file(bam1) into bwt2_merged_bam
+ set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
- sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
- tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
- oname = prefix.toString() - ~/(\.[0-9]+)$/
-
- """
- echo "## ${prefix}" > ${prefix}.mapstat
- echo -n "total_${tag}\t" >> ${prefix}.mapstat
- samtools view -c ${bam1} >> ${prefix}.mapstat
- echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
- samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
- echo -n "global_${tag}\t" >> ${prefix}.mapstat
- samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
- echo -n "local_${tag}\t0" >> ${prefix}.mapstat
- """
+ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
+ tag = prefix.toString() =~/_R1$|_val_1$|_1$/ ? "R1" : "R2"
+ oname = prefix.toString() - ~/(\.[0-9]+)$/
+
+ """
+ echo "## ${prefix}" > ${prefix}.mapstat
+ echo -n "total_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c ${bam1} >> ${prefix}.mapstat
+ echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+ echo -n "global_${tag}\t" >> ${prefix}.mapstat
+ samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+ echo -n "local_${tag}\t0" >> ${prefix}.mapstat
+ """
}
}
@@ -564,26 +564,26 @@ process combine_mapped_files{
saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
input:
- set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple()
+ set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple()
output:
- set val(sample), file("${sample}_bwt2pairs.bam") into paired_bam
- set val(oname), file("*.pairstat") into all_pairstat
+ set val(sample), file("${sample}_bwt2pairs.bam") into paired_bam
+ set val(oname), file("*.pairstat") into all_pairstat
script:
- r1_bam = aligned_bam[0]
- r1_prefix = r1_bam.toString() - ~/_bwt2merged.bam$/
- r2_bam = aligned_bam[1]
- r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/
- oname = sample.toString() - ~/(\.[0-9]+)$/
-
- def opts = "-t"
- opts = params.rm_singleton ? "${opts}" : "--single ${opts}"
- opts = params.rm_multi ? "${opts}" : "--multi ${opts}"
- if ("$params.min_mapq".isInteger()) opts="${opts} -q ${params.min_mapq}"
- """
- mergeSAM.py -f ${r1_bam} -r ${r2_bam} -o ${sample}_bwt2pairs.bam ${opts}
- """
+ r1_bam = aligned_bam[0]
+ r1_prefix = r1_bam.toString() - ~/_bwt2merged.bam$/
+ r2_bam = aligned_bam[1]
+ r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/
+ oname = sample.toString() - ~/(\.[0-9]+)$/
+
+ def opts = "-t"
+ opts = params.rm_singleton ? "${opts}" : "--single ${opts}"
+ opts = params.rm_multi ? "${opts}" : "--multi ${opts}"
+ if ("$params.min_mapq".isInteger()) opts="${opts} -q ${params.min_mapq}"
+ """
+ mergeSAM.py -f ${r1_bam} -r ${r2_bam} -o ${sample}_bwt2pairs.bam ${opts}
+ """
}
@@ -598,34 +598,33 @@ if (!params.dnase){
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"}
input:
- set val(sample), file(pe_bam) from paired_bam
- file frag_file from res_frag_file.collect()
+ set val(sample), file(pe_bam) from paired_bam
+ file frag_file from res_frag_file.collect()
output:
- set val(sample), file("*.validPairs") into valid_pairs
- set val(sample), file("*.validPairs") into valid_pairs_4cool
- set val(sample), file("*.DEPairs") into de_pairs
- set val(sample), file("*.SCPairs") into sc_pairs
- set val(sample), file("*.REPairs") into re_pairs
- set val(sample), file("*.FiltPairs") into filt_pairs
- set val(sample), file("*RSstat") into all_rsstat
+ set val(sample), file("*.validPairs") into valid_pairs
+ set val(sample), file("*.validPairs") into valid_pairs_4cool
+ set val(sample), file("*.DEPairs") into de_pairs
+ set val(sample), file("*.SCPairs") into sc_pairs
+ set val(sample), file("*.REPairs") into re_pairs
+ set val(sample), file("*.FiltPairs") into filt_pairs
+ set val(sample), file("*RSstat") into all_rsstat
script:
- if (params.splitFastq){
- sample = sample.toString() - ~/(\.[0-9]+)$/
- }
-
- def opts = ""
- if ("$params.min_cis_dist".isInteger()) opts="${opts} -d ${params.min_cis_dist}"
- if ("$params.min_insert_size".isInteger()) opts="${opts} -s ${params.min_insert_size}"
- if ("$params.max_insert_size".isInteger()) opts="${opts} -l ${params.max_insert_size}"
- if ("$params.min_restriction_fragment_size".isInteger()) opts="${opts} -t ${params.min_restriction_fragment_size}"
- if ("$params.max_restriction_fragment_size".isInteger()) opts="${opts} -m ${params.max_restriction_fragment_size}"
- if (params.saveInteractionBAM) opts="${opts} --sam"
-
- """
- mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
- """
+ if (params.splitFastq){
+ sample = sample.toString() - ~/(\.[0-9]+)$/
+ }
+
+ def opts = ""
+ if ("$params.min_cis_dist".isInteger()) opts="${opts} -d ${params.min_cis_dist}"
+ if ("$params.min_insert_size".isInteger()) opts="${opts} -s ${params.min_insert_size}"
+ if ("$params.max_insert_size".isInteger()) opts="${opts} -l ${params.max_insert_size}"
+ if ("$params.min_restriction_fragment_size".isInteger()) opts="${opts} -t ${params.min_restriction_fragment_size}"
+ if ("$params.max_restriction_fragment_size".isInteger()) opts="${opts} -m ${params.max_restriction_fragment_size}"
+ if (params.saveInteractionBAM) opts="${opts} --sam"
+ """
+ mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
+ """
}
}
else{
@@ -635,23 +634,23 @@ else{
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$filename" : "$filename"}
input:
- set val(sample), file(pe_bam) from paired_bam
+ set val(sample), file(pe_bam) from paired_bam
output:
- set val(sample), file("*.validPairs") into valid_pairs
- set val(sample), file("*.validPairs") into valid_pairs_4cool
- set val(sample), file("*RSstat") into all_rsstat
+ set val(sample), file("*.validPairs") into valid_pairs
+ set val(sample), file("*.validPairs") into valid_pairs_4cool
+ set val(sample), file("*RSstat") into all_rsstat
script:
- if (params.splitFastq){
- sample = sample.toString() - ~/(\.[0-9]+)$/
- }
-
- def opts = ""
- if ("$params.min_cis_dist".isInteger()) opts="${opts} -d ${params.min_cis_dist}"
- """
- mapped_2hic_dnase.py -r ${pe_bam} ${opts}
- """
+ if (params.splitFastq){
+ sample = sample.toString() - ~/(\.[0-9]+)$/
+ }
+
+ def opts = ""
+ if ("$params.min_cis_dist".isInteger()) opts="${opts} -d ${params.min_cis_dist}"
+ """
+ mapped_2hic_dnase.py -r ${pe_bam} ${opts}
+ """
}
}
@@ -666,12 +665,12 @@ process remove_duplicates {
saveAs: {filename -> filename.indexOf("*stat") > 0 ? "stats/$sample/$filename" : "$filename"}
input:
- set val(sample), file(vpairs) from valid_pairs.groupTuple()
+ set val(sample), file(vpairs) from valid_pairs.groupTuple()
output:
- set val(sample), file("*.allValidPairs") into all_valid_pairs
- set val(sample), file("*.allValidPairs") into all_valid_pairs_4cool
- file("stats/") into all_mergestat
+ set val(sample), file("*.allValidPairs") into all_valid_pairs
+ set val(sample), file("*.allValidPairs") into all_valid_pairs_4cool
+ file("stats/") into all_mergestat
script:
if ( params.rm_dup ){
@@ -711,21 +710,21 @@ process merge_sample {
publishDir "${params.outdir}/hic_results/stats/${sample}", mode: 'copy'
input:
- set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
+ set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
- output:
- file("mstats/") into all_mstats
+ output:
+ file("mstats/") into all_mstats
- script:
- sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
- if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
- if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
- if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
+ script:
+ sample = prefix.toString() - ~/(_R1$|_R2$|_val_1$|_val_2$|_1$|_2$)/
+ if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
+ if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
+ if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
- """
- mkdir -p mstats/${sample}
- merge_statfiles.py -f ${fstat} > mstats/${sample}/${prefix}.${ext}
- """
+ """
+ mkdir -p mstats/${sample}
+ merge_statfiles.py -f ${fstat} > mstats/${sample}/${prefix}.${ext}
+ """
}
@@ -734,15 +733,15 @@ process build_contact_maps{
publishDir "${params.outdir}/hic_results/matrix/raw", mode: 'copy'
when:
- !params.skipMaps
+ !params.skipMaps
input:
- set val(sample), file(vpairs), val(mres) from all_valid_pairs.combine(map_res)
- file chrsize from chromosome_size.collect()
+ set val(sample), file(vpairs), val(mres) from all_valid_pairs.combine(map_res)
+ file chrsize from chromosome_size.collect()
output:
- file("*.matrix") into raw_maps
- file "*.bed"
+ file("*.matrix") into raw_maps
+ file "*.bed"
script:
"""
@@ -759,14 +758,14 @@ process run_ice{
publishDir "${params.outdir}/hic_results/matrix/iced", mode: 'copy'
when:
- !params.skipMaps && !params.skipIce
+ !params.skipMaps && !params.skipIce
input:
- file(rmaps) from raw_maps
- file "*.biases"
+ file(rmaps) from raw_maps
+ file "*.biases"
output:
- file("*iced.matrix") into iced_maps
+ file("*iced.matrix") into iced_maps
script:
prefix = rmaps.toString() - ~/(\.matrix)?$/
@@ -787,14 +786,14 @@ process generate_cool{
publishDir "${params.outdir}/export/cool", mode: 'copy'
when:
- !params.skipCool
+ !params.skipCool
input:
- set val(sample), file(vpairs) from all_valid_pairs_4cool
- file chrsize from chromosome_size_cool.collect()
+ set val(sample), file(vpairs) from all_valid_pairs_4cool
+ file chrsize from chromosome_size_cool.collect()
output:
- file("*mcool") into cool_maps
+ file("*mcool") into cool_maps
script:
"""
@@ -807,28 +806,27 @@ process generate_cool{
* STEP 6 - MultiQC
*/
process multiqc {
- publishDir "${params.outdir}/MultiQC", mode: 'copy'
+ publishDir "${params.outdir}/MultiQC", mode: 'copy'
- when:
- !params.skipMultiQC
-
- input:
- file multiqc_config from ch_multiqc_config
- file ('input_*/*') from all_mstats.concat(all_mergestat).collect()
- file ('software_versions/*') from software_versions_yaml
- file workflow_summary from create_workflow_summary(summary)
+ when:
+ !params.skipMultiQC
- output:
- file "*multiqc_report.html" into multiqc_report
- file "*_data"
+ input:
+ file multiqc_config from ch_multiqc_config
+ file ('input_*/*') from all_mstats.concat(all_mergestat).collect()
+ file ('software_versions/*') from software_versions_yaml
+ file workflow_summary from create_workflow_summary(summary)
- script:
- rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
- rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
+ output:
+ file "*multiqc_report.html" into multiqc_report
+ file "*_data"
- """
- multiqc -f $rtitle $rfilename --config $multiqc_config .
- """
+ script:
+ rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
+ rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
+ """
+ multiqc -f $rtitle $rfilename --config $multiqc_config .
+ """
}
@@ -837,18 +835,18 @@ process multiqc {
* STEP 7 - Output Description HTML
*/
process output_documentation {
- publishDir "${params.outdir}/pipeline_info", mode: 'copy'
+ publishDir "${params.outdir}/pipeline_info", mode: 'copy'
- input:
- file output_docs from ch_output_docs
+ input:
+ file output_docs from ch_output_docs
- output:
- file "results_description.html"
+ output:
+ file "results_description.html"
- script:
- """
- markdown_to_html.r $output_docs results_description.html
- """
+ script:
+ """
+ markdown_to_html.r $output_docs results_description.html
+ """
}
--
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