From fa6ec7324596ee0b0c9f36b3e7f9510a763c0d0e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Oct 2021 16:49:11 +0200
Subject: [PATCH] danpos: change channel cardinality
---
src/nf_modules/danpos/main.nf | 64 ++++++++++++++++++-----------------
src/nf_modules/ucsc/main.nf | 27 +++++++++++++++
2 files changed, 60 insertions(+), 31 deletions(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 350449e9..10d42f49 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -2,7 +2,7 @@ version = "v2.2.2_cv3"
container_url = "biocontainers/danpos:${version}"
include {
- bigwig_to_wig
+ bigwig2_to_wig2
} from "./../ucsc/main.nf"
params.dpos = "--smooth_width 0 -n N "
@@ -18,8 +18,7 @@ process dpos_bam {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(bam_ip)
- tuple val(file_id), path(bam_wce)
+ tuple val(file_id), path(bam_ip), path(bam_wce)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
@@ -55,10 +54,9 @@ danpos.py dpos -m ${m}
workflow dpos_bw {
take:
fastq
- bw_ip
- bw_wce
+ bw
main:
- dpos_wig(fastq, bigwig_to_wig(bw_ip), bigwig_to_wig(bw_wce))
+ dpos_wig(fastq, bigwig2_to_wig2(bw))
emit:
wig = dpos_wig.out.wig
folder = dpos_wig.out.folder
@@ -74,8 +72,7 @@ process dpos_wig {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(wig_ip)
- tuple val(file_id), path(wig_wce)
+ tuple val(file_id), path(wig_ip), path(wig_wce)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
@@ -108,6 +105,22 @@ danpos.py dpos -m ${m}
"""
}
+workflow dwig_bwvsbw {
+ take:
+ fastq
+ bw_a
+ bw_b
+ main:
+ dpos_wigvswig(
+ fastq,
+ bigwig2_to_wig2(bw_a),
+ bigwig2_to_wig2(bw_b),
+ )
+ emit:
+ wig = dpeak_wig.out.wig
+ folder = dpeak_wig.out.folder
+}
+
process dpos_wigvswig {
container = "${container_url}"
label "big_mem_mono_cpus"
@@ -118,10 +131,8 @@ process dpos_wigvswig {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(wig_ip_a)
- tuple val(file_id), path(wig_wce_a)
- tuple val(file_id), path(wig_ip_b)
- tuple val(file_id), path(wig_wce_b)
+ tuple val(file_id), path(wig_ip_a), path(wig_wce_a)
+ tuple val(file_id), path(wig_ip_b), path(wig_wce_b)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
@@ -167,8 +178,7 @@ process dpeak_bam {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(bam_ip)
- tuple val(file_id), path(bam_wce)
+ tuple val(file_id), path(bam_ip), path(bam_wce)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
@@ -204,10 +214,9 @@ danpos.py dpeak -m ${m}
workflow dpeak_bw {
take:
fastq
- bw_ip
- bw_wce
+ bw
main:
- dpeak_wig(fastq, bigwig_to_wig(bw_ip), bigwig_to_wig(bw_wce))
+ dpeak_wig(fastq, bigwig2_to_wig2(bw))
emit:
wig = dpeak_wig.out.wig
folder = dpeak_wig.out.folder
@@ -224,8 +233,7 @@ process dpeak_wig {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(wig_ip)
- tuple val(file_id), path(wig_wce)
+ tuple val(file_id), path(wig_ip), path(wig_wce)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
@@ -261,17 +269,13 @@ danpos.py dpeak -m ${m}
workflow dpeak_bwvsbw {
take:
fastq
- bw_ip_a
- bw_wce_a
- bw_ip_b
- bw_wce_b
+ bw_a
+ bw_b
main:
dpeak_wigvswig(
fastq,
- bigwig_to_wig(bw_ip_a),
- bigwig_to_wig(bw_wce_a),
- bigwig_to_wig(bw_ip_b),
- bigwig_to_wig(bw_wce_b)
+ bigwig2_to_wig2(bw_a),
+ bigwig2_to_wig2(bw_b),
)
emit:
wig = dpeak_wig.out.wig
@@ -289,10 +293,8 @@ process dpeak_wigvswig {
input:
tuple val(file_id), path(fastq)
- tuple val(file_id), path(wig_ip_a)
- tuple val(file_id), path(wig_wce_a)
- tuple val(file_id), path(wig_ip_b)
- tuple val(file_id), path(wig_wce_b)
+ tuple val(file_id), path(wig_ip_a), path(wig_wce_a)
+ tuple val(file_id), path(wig_ip_b), path(wig_wce_b)
output:
tuple file_id, "${file_prefix}/pooled/*.wig" into wig
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 7adf6a81..6e3ebc19 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -53,4 +53,31 @@ bigWigToWig ${params.bigwig_to_wig} - \
${bg} \
${bg.simpleName}.wig
"""
+}
+
+params.bigwig2_to_wig2 = ""
+params.bigwig2_to_wig2_out = ""
+process bigwig2_to_wig2 {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${file_id}"
+ if (params.bigwig_to_wig_out != "") {
+ publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(bw_a), path(bw_b)
+
+ output:
+ tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig
+
+ script:
+"""
+bigWigToWig ${params.bigwig_to_wig} - \
+ ${bw_a} \
+ ${bw_a.simpleName}.wig
+bigWigToWig ${params.bigwig_to_wig} - \
+ ${bw_b} \
+ ${bw_b.simpleName}.wig
+"""
}
\ No newline at end of file
--
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