BEDtools: add singularity to nf files

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
       }
     }
   }

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