From 86af07f962cc64ca15fe1aac060a092b99c23c0e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Sep 2021 17:43:21 +0200
Subject: [PATCH] danpos: add bg input
---
src/nf_modules/danpos/main.nf | 56 +++++++++++++++++++++++++++++++++++
1 file changed, 56 insertions(+)
diff --git a/src/nf_modules/danpos/main.nf b/src/nf_modules/danpos/main.nf
index 0b3da90e..fda86102 100644
--- a/src/nf_modules/danpos/main.nf
+++ b/src/nf_modules/danpos/main.nf
@@ -1,6 +1,11 @@
version = "v2.2.2_cv3"
container_url = "biocontainers/danpos:${version}"
+include {
+ bigwig_to_wig as bigwig_to_wig_ip;
+ bigwig_to_wig_ip as bigwig_to_wig_wce
+} from "./../ucsc/main.nf"
+
params.dpos = "--smooth_width 0 -n N "
params.dpos_out = ""
@@ -48,6 +53,20 @@ danpos.py dpos -m ${m}
"""
}
+workflow dpos_bg {
+ take:
+ fastq
+ bg_ip
+ bg_wce
+ main:
+ bigwig_to_wig_ip(bg_ip)
+ bigwig_to_wig_wce(bg_wce)
+ dpos_wig(fastq, bigwig_to_wig_ip.out.wig, bigwig_to_wig_wce.out.wig)
+ emit:
+ wig = dpos_wig.out.wig
+ folder = dpos_wig.out.folder
+}
+
process dpos_wig {
container = "${container_url}"
label "big_mem_mono_cpus"
@@ -185,6 +204,20 @@ danpos.py dpeak -m ${m}
"""
}
+workflow dpeak_bg {
+ take:
+ fastq
+ bg_ip
+ bg_wce
+ main:
+ bigwig_to_wig_ip(bg_ip)
+ bigwig_to_wig_wce(bg_wce)
+ dpeak_wig(fastq, bigwig_to_wig_ip.out.wig, bigwig_to_wig_wce.out.wig)
+ emit:
+ wig = dpeak_wig.out.wig
+ folder = dpeak_wig.out.folder
+}
+
process dpeak_wig {
container = "${container_url}"
label "big_mem_mono_cpus"
@@ -229,6 +262,29 @@ danpos.py dpeak -m ${m}
"""
}
+workflow dpeak_bgvsbg {
+ take:
+ fastq
+ bg_ip_a
+ bg_wce_a
+ bg_ip_b
+ bg_wce_b
+ main:
+ bigwig_to_wig_ip(bg_ip)
+ bigwig_to_wig_wce(bg_wce)
+ dpeak_wigvswig(
+ fastq,
+ bigwig_to_wig_ip(bg_ip_a).out.wig,
+ bigwig_to_wig_wce(bg_wce_a).out.wig,
+ bigwig_to_wig_ip(bg_ip_b).out.wig,
+ bigwig_to_wig_wce(bg_wce_b).out.wig
+ )
+ emit:
+ wig = dpeak_wig.out.wig
+ folder = dpeak_wig.out.folder
+}
+
+
process dpeak_wigvswig {
container = "${container_url}"
label "big_mem_mono_cpus"
--
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