From 5d14ce0bf7ecf10f4d33d1380ee83bc0272ccda2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 21 Mar 2019 13:22:17 +0100
Subject: [PATCH] add tests for macs2
---
src/nf_modules/macs2/peak_calling.nf | 7 ++++++-
src/nf_modules/macs2/tests.sh | 10 ++++++++++
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/macs2/peak_calling.nf b/src/nf_modules/macs2/peak_calling.nf
index 1bd6a95..12398f2 100644
--- a/src/nf_modules/macs2/peak_calling.nf
+++ b/src/nf_modules/macs2/peak_calling.nf
@@ -2,6 +2,7 @@ params.genome_size = "hs"
params.control_tag = "control"
log.info "bam files : ${params.bam}"
log.info "genome size : ${params.genome_size}"
+log.info "control tag : ${params.control_tag}"
Channel
.fromPath( params.bam )
@@ -22,7 +23,11 @@ process peak_calling {
input:
set file_id, file(file_ip) from bam_files_ip
- set file_id_control, file(file_control) from bam_files_control.collect()
+ set file_id_control, file(file_control) from bam_files_control
+ .ifEmpty {
+ error "Cannot find any bam files matching: ${params.control_tag}"
+ }
+ .collect()
output:
file "*" into peak_output
diff --git a/src/nf_modules/macs2/tests.sh b/src/nf_modules/macs2/tests.sh
index 1491b07..fc73ce2 100755
--- a/src/nf_modules/macs2/tests.sh
+++ b/src/nf_modules/macs2/tests.sh
@@ -6,3 +6,13 @@ cp data/tiny_dataset/map/tiny_v2.bam data/tiny_dataset/map/tiny_v2_control.bam
--bam "data/tiny_dataset/map/tiny_v2*.bam" \
--genome_size 129984 \
--control_tag "control"
+
+if [ -x "$(command -v singularity)" ]; then
+ ./nextflow src/nf_modules/macs2/peak_calling.nf \
+ -c src/nf_modules/macs2/peak_calling.config \
+ -profile singularity \
+ -resume \
+ --bam "data/tiny_dataset/map/tiny_v2*.bam" \
+ --genome_size 129984 \
+ --control_tag "control"
+fi
--
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