From 48d801113c0138dbe9409f048e4cd8c08d5177b0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 26 Apr 2021 17:41:04 +0200
Subject: [PATCH] deeptools: update process params
---
src/nf_modules/deeptools/main.nf | 23 +++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index ccf3657a..52a87289 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -1,10 +1,15 @@
version = "3.1.1"
container_url = "lbmc/deeptools:${version}"
+params.index_bam = ""
+params.index_bam_out = ""
process index_bam {
container = "${container_url}"
- label "big_mem__cpus"
+ label "big_mem_multi_cpus"
tag "$file_id"
+ if (params.index_bam_out != "") {
+ publishDir "results/${params.index_bam_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam)
@@ -18,11 +23,15 @@ sambamba index -t ${task.cpus} ${bam}
"""
}
+params.bam_to_bigwig = ""
+params.bam_to_bigwig_out = ""
process bam_to_bigwig {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
-
+ if (params.bam_to_bigwig_out != "") {
+ publishDir "results/${params.bam_to_bigwig_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bam), path(idx)
@@ -37,10 +46,15 @@ bamCoverage -p ${task.cpus} --ignoreDuplicates -b ${bam} \
"""
}
+params.compute_matrix = ""
+params.compute_matrix_out = ""
process compute_matrix {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "${bed_file_id}"
+ if (params.compute_matrix_out != "") {
+ publishDir "results/${params.compute_matrix_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(bw)
@@ -60,10 +74,15 @@ computeMatrix scale-regions -S ${bw} \
"""
}
+params.compute_matrix = ""
+params.compute_matrix_out = ""
process plot_profile {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
+ if (params.compute_matrix_out != "") {
+ publishDir "results/${params.compute_matrix_out}", mode: 'copy'
+ }
input:
tuple val(file_id), path(matrix)
--
GitLab