From 908ee6cdfab5e59a7e1887daec4cb7e77fc9c10d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 15:16:25 +0200
Subject: [PATCH] ucsc: add chromsize for wigToBigWig
---
src/nf_modules/ucsc/main.nf | 47 +++++++++++++++++++++++++++++++++----
1 file changed, 42 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/ucsc/main.nf b/src/nf_modules/ucsc/main.nf
index 0d930492..eefc67e8 100644
--- a/src/nf_modules/ucsc/main.nf
+++ b/src/nf_modules/ucsc/main.nf
@@ -1,6 +1,10 @@
version = "407"
container_url = "lbmc/ucsc:${version}"
+include {
+ index_fasta
+} from './nf_modules/samtools/main'
+
params.bedgraph_to_bigwig = ""
params.bedgraph_to_bigwig_out = ""
process bedgraph_to_bigwig {
@@ -82,7 +86,22 @@ bedgraph_to_wig.pl --bedgraph ${bw_b.simpleName}.bg --wig ${bw_b.simpleName}.wig
params.wig_to_bigwig = ""
params.wig_to_bigwig_out = ""
-process wig_to_bigwig {
+
+workflow wig_to_bigwig {
+ take:
+ fasta
+ wig
+ main:
+ index_fasta(fasta)
+ wig_to_bigwig_sub(
+ wig,
+ index_fasta.out.index
+ )
+ emit:
+ bw = wig_to_bigwig_sub.out.bw
+}
+
+process wig_to_bigwig_sub {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
@@ -98,13 +117,29 @@ process wig_to_bigwig {
script:
"""
-wigToBigWig ${w} ${w.simpleName}.bw
+cut -f 1,2 ${fasta_idx} > ${fasta}.sizes
+wigToBigWig -clip ${w} ${fasta}.sizes ${w.simpleName}.bw
"""
}
params.wig2_to_bigwig2 = ""
params.wig2_to_bigwig2_out = ""
-process wig2_to_bigwig2 {
+
+workflow wig2_to_bigwig2 {
+ take:
+ fasta
+ wigs
+ main:
+ index_fasta(fasta)
+ wig2_to_bigwig2_sub(
+ wigs,
+ index_fasta.out.index
+ )
+ emit:
+ bw = wig2_to_bigwig2_sub.out.bw
+}
+
+process wig2_to_bigwig2_sub {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
@@ -114,13 +149,15 @@ process wig2_to_bigwig2 {
input:
tuple val(file_id), path(w_a), path(w_b)
+ tuple val(idx_id), path(fasta_idx)
output:
tuple val(file_id), path("${w_a.simpleName}.bw"), path("${w_b.simpleName}.bw"), emit: bw
script:
"""
-wigToBigWig ${w_a} ${w_a.simpleName}.bw
-wigToBigWig ${w_b} ${w_b.simpleName}.bw
+cut -f 1,2 ${fasta_idx} > ${fasta}.sizes
+wigToBigWig -clip ${w_a} ${fasta}.sizes ${w_a.simpleName}.bw
+wigToBigWig -clip ${w_b} ${fasta}.sizes ${w_b.simpleName}.bw
"""
}
\ No newline at end of file
--
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