From e9946c0dc5d585e963ce672aabe04b1dcb1a230b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 18 Oct 2021 16:25:43 +0200
Subject: [PATCH] danspo: add wig to bedgraph convertion
---
src/nf_modules/danpos/main.nf | 18 +++++++++++++++++-
1 file changed, 17 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 8998f4c8..3bcd4e6b 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -2,12 +2,28 @@ version = "v2.2.2_cv3"
container_url = "biocontainers/danpos:${version}"
include {
- bigwig2_to_wig2
+ bigwig2_to_wig2;
+ wig_to_bedgraph
} from "./../ucsc/main.nf"
params.dpos = "--smooth_width 0 -n N "
params.dpos_out = ""
+workflow dpos_bam_bg {
+ take:
+ fastq
+ bam
+
+ main:
+ dpos_bam(fastq, bam)
+ wig_to_bedgraph(dpos_bam.out.wig)
+
+ emit:
+ bedgraph = wig_to_bedgraph.out.bedgraph
+ wig = dpos_bam.out.wig
+ folder = dpos_bam.out.folder
+}
+
process dpos_bam {
container = "${container_url}"
label "big_mem_mono_cpus"
--
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