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Commit 44a7178e authored by nservant's avatar nservant
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[MODIF] fix input extension errors

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CHANGELOG.md
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......@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Fixed`
* Fix recurrent bug in input file extension (#86)
* Fix bug in `--bin_size` parameter (#85)
* `min_mapq` is ignored if `--keep_multi` is used
......
main.nf
+ 62
− 48
View file @ 44a7178e
......@@ -157,26 +157,36 @@ if (params.input_paths){
.from( params.input_paths )
.map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
}else{
}else{
raw_reads = Channel.create()
raw_reads_2 = Channel.create()
Channel
.fromFilePairs( params.input )
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0], a[1][0]), tuple(a[0], a[1][1])] }
if ( params.split_fastq ){
Channel
.fromFilePairs( params.input, flat:true )
.splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1]), tuple(a[0] + "_R2", a[2])] }
}else{
Channel
.fromFilePairs( params.input )
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1][0]), tuple(a[0] + "_R2", a[1][1])] }
}
}
// SPlit fastq files
// https://www.nextflow.io/docs/latest/operator.html#splitfastq
if ( params.split_fastq ){
raw_reads_full = raw_reads.concat( raw_reads_2 )
raw_reads = raw_reads_full.splitFastq( by: params.fastq_chunks_size, file: true)
}else{
raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag: "data")
// Update sample name if splitFastq is used
def updateSampleName(x) {
if ((matcher = x[1] =~ /\s*(\.[\d]+).fastq.gz/)) {
res = matcher[0][1]
}
return [x[0] + res, x[1]]
}
if (params.split_fastq ){
raw_reads = raw_reads.concat( raw_reads_2 ).map{it -> updateSampleName(it)}.dump(tag:'input')
}else{
raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag:'input')
}
/*
* Other input channels
......@@ -230,7 +240,7 @@ else if ( params.fasta && params.restriction_site ){
.ifEmpty { exit 1, "Restriction fragments: Fasta file not found: ${params.fasta}" }
.set { fasta_for_resfrag }
}
else {
else if (! params.dnase) {
exit 1, "No restriction fragments file specified!"
}
......@@ -255,17 +265,17 @@ if (params.restriction_site){
summary['Digestion'] = params.digestion
summary['Restriction Motif']= params.restriction_site
summary['Ligation Motif'] = params.ligation_site
summary['Min Fragment Size']= ("$params.min_restriction_fragment_size".isInteger() ? params.min_restriction_fragment_size : 'None')
summary['Max Fragment Size']= ("$params.max_restriction_fragment_size".isInteger() ? params.max_restriction_fragment_size : 'None')
summary['Min Insert Size'] = ("$params.min_insert_size".isInteger() ? params.min_insert_size : 'None')
summary['Max Insert Size'] = ("$params.max_insert_size".isInteger() ? params.max_insert_size : 'None')
summary['Min Fragment Size']= params.min_restriction_fragment_size
summary['Max Fragment Size']= params.max_restriction_fragment_size
summary['Min Insert Size'] = params.min_insert_size
summary['Max Insert Size'] = params.max_insert_size
}else{
summary['DNase Mode'] = params.dnase
summary['Min CIS dist'] = ("$params.min_cis_dist".isInteger() ? params.min_cis_dist : 'None')
summary['Min CIS dist'] = params.min_cis_dist
}
summary['Min MAPQ'] = params.min_mapq
summary['Keep Duplicates'] = params.keep_dups
summary['Keep Multihits'] = params.keep_multi
summary['Keep Duplicates'] = params.keep_dups ? 'Yes' : 'No'
summary['Keep Multihits'] = params.keep_multi ? 'Yes' : 'No'
summary['Maps resolution'] = params.bin_size
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
......@@ -435,7 +445,7 @@ if(!params.restriction_fragments && params.fasta && !params.dnase){
*/
process bowtie2_end_to_end {
tag "$prefix"
tag "$sample"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
......@@ -445,13 +455,12 @@ process bowtie2_end_to_end {
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(sample), file("${prefix}_unmap.fastq") into unmapped_end_to_end
set val(sample), file("${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} \\
......@@ -474,7 +483,7 @@ process bowtie2_end_to_end {
}
process trim_reads {
tag "$prefix"
tag "$sample"
label 'process_low'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
......@@ -483,12 +492,13 @@ process trim_reads {
!params.dnase
input:
set val(prefix), file(reads) from unmapped_end_to_end
set val(sample), file(reads) from unmapped_end_to_end
output:
set val(prefix), file("${prefix}_trimmed.fastq") into trimmed_reads
set val(sample), file("${prefix}_trimmed.fastq") into trimmed_reads
script:
prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
"""
cutsite_trimming --fastq $reads \\
--cutsite ${params.ligation_site} \\
......@@ -497,7 +507,7 @@ process trim_reads {
}
process bowtie2_on_trimmed_reads {
tag "$prefix"
tag "$sample"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
......@@ -506,11 +516,11 @@ process bowtie2_on_trimmed_reads {
!params.dnase
input:
set val(prefix), file(reads) from trimmed_reads
set val(sample), file(reads) from trimmed_reads
file index from bwt2_index_trim.collect()
output:
set val(prefix), file("${prefix}_trimmed.bam") into trimmed_bam
set val(sample), file("${prefix}_trimmed.bam") into trimmed_bam
script:
prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
......@@ -524,22 +534,24 @@ process bowtie2_on_trimmed_reads {
}
if (!params.dnase){
process merge_mapping_steps{
tag "$sample = $bam1 + $bam2"
process bowtie2_merge_mapping_steps{
tag "$prefix = $bam1 + $bam2"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
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 ).dump(tag:'merge')
output:
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"
//sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
sample = prefix.toString() - ~/(_R1|_R2)/
//tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
samtools merge -@ ${task.cpus} \\
......@@ -566,46 +578,48 @@ if (!params.dnase){
}
}else{
process dnase_mapping_stats{
tag "$sample = $bam1"
tag "$sample = $bam"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
input:
set val(prefix), file(bam1) from end_to_end_bam
set val(prefix), file(bam) from end_to_end_bam
output:
set val(sample), file(bam1) into bwt2_merged_bam
set val(sample), file(bam) into bwt2_merged_bam
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
//sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
sample = prefix.toString() - ~/(_R1|_R2)/
//tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
echo "## ${prefix}" > ${prefix}.mapstat
echo -n "total_${tag}\t" >> ${prefix}.mapstat
samtools view -c ${bam1} >> ${prefix}.mapstat
samtools view -c ${bam} >> ${prefix}.mapstat
echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
echo -n "global_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
echo -n "local_${tag}\t0" >> ${prefix}.mapstat
"""
}
}
process combine_mapped_files{
process combine_mates{
tag "$sample = $r1_prefix + $r2_prefix"
label 'process_low'
publishDir "${params.outdir}/mapping", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
input:
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'bams')
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'mates')
output:
set val(sample), file("${sample}_bwt2pairs.bam") into paired_bam
set val(oname), file("${sample}_bwt2pairs.bam") into paired_bam
set val(oname), file("*.pairstat") into all_pairstat
script:
......@@ -629,7 +643,7 @@ process combine_mapped_files{
/*
* STEP2 - DETECT VALID PAIRS
*/
*/
if (!params.dnase){
process get_valid_interaction{
......@@ -711,7 +725,7 @@ 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().dump(tag:'final')
output:
set val(sample), file("*.allValidPairs") into all_valid_pairs
......
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