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Verified Commit ac7209ac authored by Laurent Modolo's avatar Laurent Modolo
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danpos: re-add wce for dpos_bam

parent c3010d1a
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...@@ -17,10 +17,10 @@ workflow dpos_bam_bg { ...@@ -17,10 +17,10 @@ workflow dpos_bam_bg {
main: main:
dpos_bam(fastq, bam) dpos_bam(fastq, bam)
wig_to_bedgraph(dpos_bam.out.wig) wig2_to_bedgraph2(dpos_bam.out.wig)
emit: emit:
bedgraph = wig_to_bedgraph.out.bedgraph bedgraph = wig2_to_bedgraph2.out.bedgraph
wig = dpos_bam.out.wig wig = dpos_bam.out.wig
bed = dpos_bam.out.bed bed = dpos_bam.out.bed
folder = dpos_bam.out.folder folder = dpos_bam.out.folder
...@@ -36,10 +36,10 @@ process dpos_bam { ...@@ -36,10 +36,10 @@ process dpos_bam {
input: input:
tuple val(fastq_id), path(fastq) tuple val(fastq_id), path(fastq)
tuple val(file_id), path(bam_ip) tuple val(file_id), path(bam_ip), path(bam_wce)
output: output:
tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), emit: wig tuple val(file_id), path("${file_prefix}/${bam_ip.simpleName}*.wig"), path("${file_prefix}/${bam_wce.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed tuple val(file_id), path("${file_prefix}/*.positions.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder tuple val(file_id), path("${file_prefix}"), emit: folder
...@@ -64,6 +64,7 @@ process dpos_bam { ...@@ -64,6 +64,7 @@ process dpos_bam {
""" """
danpos.py dpos -m ${m} \ danpos.py dpos -m ${m} \
${params.dpos} \ ${params.dpos} \
-b ${bam_wce}
-o ${file_prefix} \ -o ${file_prefix} \
${bam_ip} ${bam_ip}
mv ${file_prefix}/pooled/* ${file_prefix}/ mv ${file_prefix}/pooled/* ${file_prefix}/
......
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