From d0a65940994410d347985cbc2f9706b9f695803c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Mar 2019 17:27:14 +0100
Subject: [PATCH] bwa: fix warining in tests
---
src/nf_modules/bedtools/fasta_from_bed.config | 2 +-
src/nf_modules/bwa/tests.sh | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index c1ac99f1..0a70980b 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -12,7 +12,7 @@ profiles {
singularity {
singularity.enabled = true
process {
- withName: trimming {
+ withName: fasta_from_bed {
container = "file://bin/bedtools:2.25.0.sif"
cpus = 1
}
diff --git a/src/nf_modules/bwa/tests.sh b/src/nf_modules/bwa/tests.sh
index 2125e6c3..e601d200 100755
--- a/src/nf_modules/bwa/tests.sh
+++ b/src/nf_modules/bwa/tests.sh
@@ -13,7 +13,7 @@
./nextflow src/nf_modules/bwa/mapping_paired.nf \
-c src/nf_modules/bwa/mapping_paired.config \
-profile docker \
- --index "results/mapping/index/tiny_v2*" \
+ --index "results/mapping/index/tiny_v2.*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
@@ -35,7 +35,7 @@ if [ -x "$(command -v singularity)" ]; then
./nextflow src/nf_modules/bwa/mapping_paired.nf \
-c src/nf_modules/bwa/mapping_paired.config \
-profile singularity \
- --index "results/mapping/index/tiny_v2*" \
+ --index "results/mapping/index/tiny_v2.*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
-resume
--
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