From 014698120c192b06a4560040b029a073b58684d2 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Tue, 30 Apr 2019 09:56:31 +0200
Subject: [PATCH] add --skip options
---
main.nf | 8 ++++++++
nextflow.config | 2 ++
2 files changed, 10 insertions(+)
diff --git a/main.nf b/main.nf
index 5550fb1..4b975d0 100644
--- a/main.nf
+++ b/main.nf
@@ -75,6 +75,8 @@ def helpMessage() {
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
Step options:
+ --skip_maps Skip generation of contact maps. Useful for capture-C
+ --skip_ice Skip ICE normalization
--skip_cool Skip generation of cool files
--skip_multiQC Skip MultiQC
@@ -720,6 +722,9 @@ process build_contact_maps{
tag "$sample - $mres"
publishDir "${params.outdir}/hic_results/matrix/raw", mode: 'copy'
+ when:
+ !params.skip_maps
+
input:
set val(sample), file(vpairs), val(mres) from all_valid_pairs.combine(map_res)
file chrsize from chromosome_size.collect()
@@ -742,6 +747,9 @@ process run_ice{
tag "$rmaps"
publishDir "${params.outdir}/hic_results/matrix/iced", mode: 'copy'
+ when:
+ !params.skip_maps && !params.skip_ice
+
input:
file(rmaps) from raw_maps
file "*.biases"
diff --git a/nextflow.config b/nextflow.config
index 32486aa..e80bebe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,6 +19,8 @@ params {
readPaths = false
chromosome_size = false
restriction_fragments = false
+ skip_maps = false
+ skip_ice = false
skip_cool = false
skip_multiqc = false
dnase = false
--
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