sambamba: fix singularity path

src/nf_modules/sambamba/index_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: index_bam {
         container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'

src/nf_modules/sambamba/index_bams.nf

@@ -10,7 +10,6 @@ Channel
 
 process index_bam {
   tag "$file_id"
-  cpus 4
 
   input:
     set file_id, file(bam) from bam_files

src/nf_modules/sambamba/sort_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: sort_bam {
         container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 4
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'

src/nf_modules/sambamba/split_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: split_bam {
         container = "sambamba:0.6.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'

src/nf_modules/sambamba/tests.sh

 ./nextflow src/nf_modules/sambamba/sort_bams.nf \
   -c src/nf_modules/sambamba/sort_bams.config \
   -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
 
 ./nextflow src/nf_modules/sambamba/index_bams.nf \
   -c src/nf_modules/sambamba/index_bams.config \
   -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
 
 ./nextflow src/nf_modules/sambamba/split_bams.nf \
   -c src/nf_modules/sambamba/split_bams.config \
   -profile docker \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/sambamba/sort_bams.nf \
+  -c src/nf_modules/sambamba/sort_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/index_bams.nf \
+  -c src/nf_modules/sambamba/index_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/sambamba/split_bams.nf \
+  -c src/nf_modules/sambamba/split_bams.config \
+  -profile singularity \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi

src/singularity_modules/sambamba/0.6.7/build.sh

 #/bin/sh
-sudo singularity build --force /bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def
+sudo singularity build --force bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def