From 2901dd9fe3ca702ff558388cc77c39eaeb0e3a6d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 14:10:53 +0100
Subject: [PATCH] UrQt: add singularity config and test
---
src/nf_modules/UrQt/tests.sh | 12 ++++++++++++
src/nf_modules/UrQt/trimming_paired.config | 8 ++++++++
src/nf_modules/UrQt/trimming_single.config | 8 ++++++++
3 files changed, 28 insertions(+)
diff --git a/src/nf_modules/UrQt/tests.sh b/src/nf_modules/UrQt/tests.sh
index 96f58453..2c510d78 100755
--- a/src/nf_modules/UrQt/tests.sh
+++ b/src/nf_modules/UrQt/tests.sh
@@ -7,3 +7,15 @@
-c src/nf_modules/UrQt/trimming_single.config \
-profile docker \
--fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/UrQt/trimming_single.nf \
+ -c src/nf_modules/UrQt/trimming_single.config \
+ -profile singularity \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+./nextflow src/nf_modules/UrQt/trimming_single.nf \
+ -c src/nf_modules/UrQt/trimming_single.config \
+ -profile singularity \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+fi
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
index cc928803..dd40a8ba 100644
--- a/src/nf_modules/UrQt/trimming_paired.config
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -8,6 +8,14 @@ profiles {
}
}
}
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: trimming {
+ container = "file:///bin/UrQt:d62c1f8.sif"
+ }
+ }
+ }
psmn {
process{
withName: trimming {
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
index cc928803..dd40a8ba 100644
--- a/src/nf_modules/UrQt/trimming_single.config
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -8,6 +8,14 @@ profiles {
}
}
}
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: trimming {
+ container = "file:///bin/UrQt:d62c1f8.sif"
+ }
+ }
+ }
psmn {
process{
withName: trimming {
--
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