From 816017118ae78ef60ec02210f320d54040af5a73 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Wed, 17 Apr 2019 19:32:52 +0200
Subject: [PATCH] fix bug in DNase mode
---
main.nf | 116 +++++++++++++++++++++++++++++++++++++++++---------------
1 file changed, 86 insertions(+), 30 deletions(-)
diff --git a/main.nf b/main.nf
index 85ac949..60fe35c 100644
--- a/main.nf
+++ b/main.nf
@@ -99,6 +99,11 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
}
+// Check Digestion or DNase Hi-C mode
+if (!params.dnase && !params.ligation_site) {
+ exit 1, "Ligation motif not found. For DNase Hi-C, please use '--dnase' option"
+}
+
// Reference index path configuration
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
@@ -403,14 +408,26 @@ process bowtie2_end_to_end {
script:
prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
def bwt2_opts = params.bwt2_opts_end2end
- """
- bowtie2 --rg-id BMG --rg SM:${prefix} \\
+
+ if (!params.dnase){
+ """
+ bowtie2 --rg-id BMG --rg SM:${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} > ${prefix}.bam
+ """
+ }
}
process trim_reads {
@@ -418,6 +435,9 @@ process trim_reads {
publishDir path: { params.saveAlignedIntermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
+ when:
+ !params.dnase
+
input:
set val(prefix), file(reads) from unmapped_end_to_end
@@ -437,6 +457,9 @@ process bowtie2_on_trimmed_reads {
publishDir path: { params.saveAlignedIntermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
+ when:
+ !params.dnase
+
input:
set val(prefix), file(reads) from trimmed_reads
file index from bwt2_index_trim.collect()
@@ -455,47 +478,80 @@ process bowtie2_on_trimmed_reads {
"""
}
-process merge_mapping_steps{
- tag "$sample = $bam1 + $bam2"
- publishDir path: { params.saveAlignedIntermediates ? "${params.outdir}/mapping" : params.outdir },
+if (!params.dnase){
+ process merge_mapping_steps{
+ tag "$sample = $bam1 + $bam2"
+ publishDir path: { params.saveAlignedIntermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
- input:
- set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam )
+ input:
+ 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
+ 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)/
- tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
- oname = prefix.toString() - ~/(\.[0-9]+)$/
+ script:
+ sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/
+ tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
+ oname = prefix.toString() - ~/(\.[0-9]+)$/
- """
- samtools merge -@ ${task.cpus} \\
+ """
+ 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} >> ${prefix}.mapstat
+ """
+ }
+}else{
+ process dnase_mapping_stats{
+ tag "$sample = $bam1"
+ publishDir path: { params.saveAlignedIntermediates ? "${params.outdir}/mapping" : params.outdir },
+ saveAs: { params.saveAlignedIntermediates ? it : null }, mode: 'copy'
+
+ input:
+ set val(prefix), file(bam1) from end_to_end_bam
+
+ output:
+ set val(sample), file(bam1) into bwt2_merged_bam
+ set val(oname), file("${prefix}.mapstat") into all_mapstat
+
+ script:
+ sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2)/
+ tag = prefix.toString() =~/_R1|_val_1/ ? "R1" : "R2"
+ oname = prefix.toString() - ~/(\.[0-9]+)$/
+
+ """
+ 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" >> ${prefix}.mapstat
+ """
+ }
}
+
+
process combine_mapped_files{
tag "$sample = $r1_prefix + $r2_prefix"
publishDir "${params.outdir}/mapping", mode: 'copy',
--
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