From cf94bb20ba196154fd0c3e08f8062489af716e02 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 29 Aug 2018 10:48:03 +0200
Subject: [PATCH] MUSIC: add tests.sh file to run the tests
---
.../MUSIC/peak_calling_paired.config | 30 -------------------
src/nf_modules/MUSIC/tests.sh | 8 +++++
src/training_dataset.nf | 4 +--
3 files changed, 10 insertions(+), 32 deletions(-)
delete mode 100644 src/nf_modules/MUSIC/peak_calling_paired.config
create mode 100755 src/nf_modules/MUSIC/tests.sh
diff --git a/src/nf_modules/MUSIC/peak_calling_paired.config b/src/nf_modules/MUSIC/peak_calling_paired.config
deleted file mode 100644
index 4685752..0000000
--- a/src/nf_modules/MUSIC/peak_calling_paired.config
+++ /dev/null
@@ -1,30 +0,0 @@
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $compute_mappability {
- container = "music:6613c53"
- }
- $music_preprocessing {
- container = "music:6613c53"
- }
- $music_computation {
- container = "music:6613c53"
- }
- }
- }
- sge {
- process{
- $compute_mappability {
- beforeScript = "module purge; module load MUSIC/6613c53"
- }
- $music_preprocessing {
- beforeScript = "module purge; module load MUSIC/6613c53"
- }
- $music_computation {
- beforeScript = "module purge; module load MUSIC/6613c53"
- }
- }
- }
-}
diff --git a/src/nf_modules/MUSIC/tests.sh b/src/nf_modules/MUSIC/tests.sh
new file mode 100755
index 0000000..7c6ad07
--- /dev/null
+++ b/src/nf_modules/MUSIC/tests.sh
@@ -0,0 +1,8 @@
+cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
+./nextflow src/nf_modules/MUSIC/peak_calling_single.nf \
+ -c src/nf_modules/MUSIC/peak_calling_single.config \
+ -profile docker \
+ --fasta "results/training/fasta/*.fasta" \
+ --bam "results/training/bams/s*.bam" \
+ --index "results/training/mapping/index/*" \
+ --read_size 50 --frag_size 300
diff --git a/src/training_dataset.nf b/src/training_dataset.nf
index 7796067..c6f48e8 100644
--- a/src/training_dataset.nf
+++ b/src/training_dataset.nf
@@ -147,7 +147,7 @@ if ( params.fastq_paired != "" ) {
set file_id, "*.fastq" into fastq_files_extracted
script:
"""
- samtools fastq -1 s${file_id}_R1.fastq -2 s${file_id}_R2.fastq -f 0x2 ${bam}
+ samtools fastq -1 s${file_id}_R1.fastq -2 s${file_id}_R2.fastq -F 0x4 ${bam}
"""
}
@@ -163,7 +163,7 @@ if ( params.fastq_paired != "" ) {
set file_id, "*.bam" into filtered_bam_files_paired
script:
"""
- samtools view -@ ${task.cpus} -hb ${bam} -f 0x2 > f${file_id}.bam
+ samtools view -@ ${task.cpus} -hb ${bam} -F 0x4 > f${file_id}.bam
"""
}
--
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