From f1a4275ccf0c456bf5c010d2ddb5c0d3001e0d52 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 1 Mar 2019 15:24:03 +0100
Subject: [PATCH] BEDtools: add singularity to nf files
---
src/nf_modules/BEDtools/fasta_from_bed.config | 10 ++++++++++
src/nf_modules/BEDtools/tests.sh | 10 ++++++++++
2 files changed, 20 insertions(+)
diff --git a/src/nf_modules/BEDtools/fasta_from_bed.config b/src/nf_modules/BEDtools/fasta_from_bed.config
index 72c98899..47a8bd94 100644
--- a/src/nf_modules/BEDtools/fasta_from_bed.config
+++ b/src/nf_modules/BEDtools/fasta_from_bed.config
@@ -5,6 +5,16 @@ profiles {
process {
withName: fasta_from_bed {
container = "bedtools:2.25.0"
+ cpus = 1
+ }
+ }
+ }
+ singularity {
+ singularity.enabled = true
+ process {
+ withName: trimming {
+ container = "file:///bin/bedtools:2.25.0.sif"
+ cpus = 1
}
}
}
diff --git a/src/nf_modules/BEDtools/tests.sh b/src/nf_modules/BEDtools/tests.sh
index 632ba5bf..d493cdea 100755
--- a/src/nf_modules/BEDtools/tests.sh
+++ b/src/nf_modules/BEDtools/tests.sh
@@ -3,3 +3,13 @@
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--bed "data/tiny_dataset/annot/tiny.bed" \
+ -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/BEDtools/fasta_from_bed.nf \
+ -c src/nf_modules/BEDtools/fasta_from_bed.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ --bed "data/tiny_dataset/annot/tiny.bed" \
+ -resume
+fi
--
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