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Verified Commit 189e58db authored by Laurent Modolo's avatar Laurent Modolo
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danpos: remove wce for dpos to follow recommandations

parent 3f7b66ba
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......@@ -17,10 +17,10 @@ workflow dpos_bam_bg {
main:
dpos_bam(fastq, bam)
wig2_to_bedgraph2(dpos_bam.out.wig)
wig_to_bedgraph(dpos_bam.out.wig)
emit:
bedgraph = wig2_to_bedgraph2.out.bedgraph
bedgraph = wig_to_bedgraph.out.bedgraph
wig = dpos_bam.out.wig
bed = dpos_bam.out.bed
folder = dpos_bam.out.folder
......@@ -36,10 +36,10 @@ process dpos_bam {
input:
tuple val(fastq_id), path(fastq)
tuple val(file_id), path(bam_ip), path(bam_wce)
tuple val(file_id), path(bam_ip)
output:
tuple val(file_id), path("${file_prefix}/pooled/${bam_ip.simpleName}*.wig"), path("${file_prefix}/pooled/${bam_wce.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/pooled/${bam_ip.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
......@@ -64,7 +64,6 @@ process dpos_bam {
"""
danpos.py dpos -m ${m} \
${params.dpos} \
-b ${bam_wce} \
-o ${file_prefix} \
${bam_ip}
mv ${file_prefix}/pooled/* ${file_prefix}/
......@@ -80,10 +79,10 @@ workflow dpos_bw {
bw
main:
dpos_wig(fastq, bigwig2_to_wig2(bw))
wig2_to_bedgraph2(dpos_wig.out.wig)
wig_to_bedgraph(dpos_wig.out.wig)
emit:
bedgraph = wig2_to_bedgraph2.out.bedgraph
bedgraph = wig_to_bedgraph.out.bedgraph
wig = dpos_wig.out.wig
bed = dpos_wig.out.bed
folder = dpos_wig.out.folder
......@@ -99,10 +98,10 @@ process dpos_wig {
input:
tuple val(fastq_id), path(fastq)
tuple val(file_id), path(wig_ip), path(wig_wce)
tuple val(file_id), path(wig_ip)
output:
tuple val(file_id), path("${file_prefix}/pooled/${wig_ip.simpleName}*.wig"), path("${file_prefix}/pooled/${wig_wce.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/pooled/${wig_ip.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id), path("${file_prefix}"), emit: folder
......@@ -127,7 +126,6 @@ process dpos_wig {
"""
danpos.py dpos -m ${m} \
${params.dpos} \
-b ${wig_wce} \
-o ${file_prefix} \
${wig_ip}
mv ${file_prefix}/pooled/* ${file_prefix}/
......@@ -148,10 +146,10 @@ workflow dwig_bwvsbw {
bigwig2_to_wig2(bw_a),
bigwig2_to_wig2(bw_b),
)
wig2_to_bedgraph2(dpos_wigvswig.out.wig)
wig_to_bedgraph(dpos_wigvswig.out.wig)
emit:
bedgraph = wig2_to_bedgraph2.out.bedgraph
bedgraph = wig_to_bedgraph.out.bedgraph
wig = dpeak_wig.out.wig
bed = dpeak_wig.out.bed
folder = dpeak_wig.out.folder
......@@ -167,11 +165,11 @@ process dpos_wigvswig {
input:
tuple val(fastq_id), path(fastq)
tuple val(file_id_a), path(wig_ip_a), path(wig_wce_a)
tuple val(file_id_b), path(wig_ip_b), path(wig_wce_b)
tuple val(file_id_a), path(wig_ip_a)
tuple val(file_id_b), path(wig_ip_b)
output:
tuple val(file_id), path("${file_prefix}/pooled/${wig_ip_a.simpleName}*.wig"), path("${file_prefix}/pooled/${wig_wce_a.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/pooled/${wig_ip_a.simpleName}*.wig"), emit: wig
tuple val(file_id), path("${file_prefix}/*.positions.bed"), path("${file_prefix}/*.summit.bed"), emit: bed
tuple val(file_id_a), path("${file_prefix}"), emit: folder
......@@ -196,7 +194,7 @@ process dpos_wigvswig {
"""
danpos.py dpos -m ${m} \
${params.dpos} \
-b ${wig_ip_a}:${wig_wce_a},${wig_ip_b}:${wig_wce_b} \
-b ${wig_ip_a},${wig_ip_b} \
-o ${file_prefix} \
${wig_ip_a}:${wig_ip_b}
mv ${file_prefix}/pooled/* ${file_prefix}/
......
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