From d14e7205670949b86bdb54d9cb7d991a2888cd43 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 20 Dec 2018 16:56:28 +0100
Subject: [PATCH] deepTools: add test for 2 bam files
---
src/nf_modules/deepTools/compute_matrix.nf | 7 +++----
src/nf_modules/deepTools/tests.sh | 4 +++-
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/deepTools/compute_matrix.nf b/src/nf_modules/deepTools/compute_matrix.nf
index e9de4136..d1d0ae07 100644
--- a/src/nf_modules/deepTools/compute_matrix.nf
+++ b/src/nf_modules/deepTools/compute_matrix.nf
@@ -1,4 +1,4 @@
-params.bam = "$baseDir/data/bigwig/*.bw"
+params.bw = "$baseDir/data/bigwig/*.bw"
params.bed = "$baseDir/data/annot/*.bed"
log.info "bigwig files : ${params.bw}"
@@ -7,7 +7,6 @@ log.info "bed files : ${params.bed}"
Channel
.fromPath( params.bw )
.ifEmpty { error "Cannot find any bigwig files matching: ${params.bw}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { bw_files }
Channel
@@ -17,12 +16,12 @@ Channel
.set { bed_files }
process compute_matrix {
- tag "$file_id"
+ tag "$bed_file_id"
cpus 4
publishDir "results/mapping/region_matrix/", mode: 'copy'
input:
- set bw_file_id, file(bw) from bw_files.collect()
+ file bw from bw_files.collect()
set bed_file_id, file(bed) from bed_files.collect()
output:
diff --git a/src/nf_modules/deepTools/tests.sh b/src/nf_modules/deepTools/tests.sh
index 06057a81..f6950b96 100755
--- a/src/nf_modules/deepTools/tests.sh
+++ b/src/nf_modules/deepTools/tests.sh
@@ -1,6 +1,8 @@
#!/bin/sh
-./nextflow src/nf_modules/deepTools/bam_to_bigwig.nf -c src/nf_modules/deepTools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_bis.sort.bam
+
+./nextflow src/nf_modules/deepTools/bam_to_bigwig.nf -c src/nf_modules/deepTools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2*.sort.bam"
./nextflow src/nf_modules/deepTools/compute_matrix.nf -c src/nf_modules/deepTools/compute_matrix.config -profile docker --bw "results/mapping/bigwig/*.bw" --bed "data/tiny_dataset/annot/tiny.bed"
--
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