nf_modules: add singularity in config files and tests.sh

src/nf_modules/samblaster/dedup_sams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: dedup_sam {
         container = "samblaster:0.1.24"
+        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 = "samblaster/0.1.24"
         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/samblaster/dedup_sams.nf

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

src/nf_modules/samblaster/tests.sh

@@ -3,3 +3,11 @@
   -profile docker \
   --bam "data/tiny_dataset/map/tiny_v2.bam" \
   -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/samblaster/dedup_sams.nf \
+  -c src/nf_modules/samblaster/dedup_sams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi

src/nf_modules/samtools/filter_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: filter_bam {
         container = "samtools:1.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: filter_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
     }
   }
@@ -15,9 +25,11 @@ profiles {
         module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }

src/nf_modules/samtools/filter_bams.nf

@@ -16,7 +16,6 @@ Channel
 
 process filter_bam {
   tag "$file_id"
-  cpus 4
 
   input:
     set file_id, file(bam) from bam_files

src/nf_modules/samtools/index_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: index_bam {
         container = "samtools:1.7"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/samtools/sort_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: sort_bam {
         container = "samtools:1.7"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 4
       }
     }
   }
@@ -15,9 +25,11 @@ profiles {
         module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
-        memory = "20GB"
-        time = "12h"
-        queue = 'monointeldeb128'
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
       }
     }
   }

src/nf_modules/samtools/sort_bams.nf

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

src/nf_modules/samtools/split_bams.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: split_bam {
         container = "samtools:1.7"
+        cpus = 2
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/samtools:1.7.sif"
+        cpus = 2
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/samtools/split_bams.nf

@@ -10,7 +10,6 @@ Channel
 
 process split_bam {
   tag "$file_id"
-  cpus 2
 
   input:
     set file_id, file(bam) from bam_files

src/nf_modules/samtools/tests.sh

@@ -22,3 +22,30 @@
   --bam "data/tiny_dataset/map/tiny_v2.bam" \
   --bed "data/tiny_dataset/OLD/2genes.bed" \
   -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/samtools/sort_bams.nf \
+  -c src/nf_modules/samtools/sort_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/index_bams.nf \
+  -c src/nf_modules/samtools/index_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/split_bams.nf \
+  -c src/nf_modules/samtools/split_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+
+./nextflow src/nf_modules/samtools/filter_bams.nf \
+  -c src/nf_modules/samtools/filter_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  --bed "data/tiny_dataset/OLD/2genes.bed" \
+  -resume
+fi

src/nf_modules/sratoolkit/fastqdump.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: fastq_dump {
         container = "sratoolkit:2.8.2"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: split_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "sratoolkit/2.8.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/sratoolkit/tests.sh

@@ -3,3 +3,11 @@
   -profile docker \
   --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
   -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/sratoolkit/fastqdump.nf \
+  -c src/nf_modules/sratoolkit/fastqdump.config \
+  -profile docker \
+  --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
+  -resume
+fi