nf_modules: add singularity in config files and tests.sh

src/nf_modules/htseq/htseq.config

@@ -5,9 +5,20 @@ profiles {
     process {
       withName: sort_bam {
         container = "samtools:1.7"
+        cpus = 1
       }
       withName: counting {
         container = "htseq:0.8.0"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: sort_bam {
+        container = "file://bin/htseq:0.8.0.sif"
+        cpus = 1
       }
     }
   }
@@ -18,6 +29,7 @@ profiles {
         module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'
@@ -27,6 +39,7 @@ profiles {
         module = "htseq/0.8.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/htseq/tests.sh

@@ -5,3 +5,11 @@
   --bam "data/tiny_dataset/map/tiny_v2.bam" \
   -resume
 
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/htseq/htseq.nf \
+  -c src/nf_modules/htseq/htseq.config \
+  -profile docker \
+  --gtf "data/tiny_dataset/annot/tiny.gff" \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
+fi

src/nf_modules/kallisto/indexing.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: index_fasta {
         container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "kallisto/0.44.0"
         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/kallisto/indexing.nf

@@ -9,7 +9,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:

src/nf_modules/kallisto/mapping_paired.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: mapping_fastq {
         container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "kallisto/0.44.0"
         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/kallisto/mapping_paired.nf

@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$reads"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:

src/nf_modules/kallisto/mapping_single.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: mapping_fastq {
         container = "kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/kallisto:0.44.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "kallisto/0.44.0"
         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/kallisto/mapping_single.nf

@@ -20,7 +20,6 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:

src/nf_modules/kallisto/tests.sh

@@ -18,3 +18,24 @@
   --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
   -resume
 
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/kallisto/indexing.nf \
+  -c src/nf_modules/kallisto/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_single.nf \
+  -c src/nf_modules/kallisto/mapping_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/kallisto/mapping_paired.nf \
+  -c src/nf_modules/kallisto/mapping_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi

src/nf_modules/multiqc/multiqc_paired.config

@@ -6,9 +6,24 @@ profiles {
     process {
       withName: fastqc_fastq {
         container = "fastqc:0.11.5"
+        cpus = 1
       }
       withName: multiqc {
         container = "multiqc:1.0"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "file://bin/fastqc:0.11.5.sif"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "file://bin/multiqc:1.0.sif"
+        cpus = 1
       }
     }
   }
@@ -19,6 +34,7 @@ profiles {
         module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "5GB"
         time = "6h"
         queueSize = 1000
@@ -30,6 +46,7 @@ profiles {
         module = "multiqc/1.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "5GB"
         time = "6h"
         queueSize = 1000

src/nf_modules/multiqc/multiqc_single.config

@@ -5,9 +5,24 @@ profiles {
     process {
       withName: fastqc_fastq {
         container = "fastqc:0.11.5"
+        cpus = 1
       }
       withName: multiqc {
         container = "multiqc:1.0"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        container = "file://bin/fastqc:0.11.5.sif"
+        cpus = 1
+      }
+      withName: multiqc {
+        container = "file://bin/multiqc:1.0.sif"
+        cpus = 1
       }
     }
   }
@@ -18,6 +33,7 @@ profiles {
         module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "5GB"
         time = "6h"
         queueSize = 1000
@@ -29,6 +45,7 @@ profiles {
         module = "multiqc/1.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "5GB"
         time = "6h"
         queueSize = 1000

src/nf_modules/multiqc/tests.sh

@@ -9,3 +9,17 @@
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
   -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/multiqc/multiqc_paired.nf \
+  -c src/nf_modules/multiqc/multiqc_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/multiqc/multiqc_single.nf \
+  -c src/nf_modules/multiqc/multiqc_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi

src/nf_modules/music/peak_calling_single.config

@@ -5,12 +5,32 @@ profiles {
     process {
       withName: compute_mappability {
         container = "music:6613c53"
+        cpus = 1
       }
       withName: music_preprocessing {
         container = "music:6613c53"
+        cpus = 1
       }
       withName: music_computation {
         container = "music:6613c53"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_mappability {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
+      }
+      withName: music_preprocessing {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
+      }
+      withName: music_computation {
+        container = "file://bin/music:6613c53.sif"
+        cpus = 1
       }
     }
   }
@@ -21,6 +41,7 @@ profiles {
         module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'
@@ -30,6 +51,7 @@ profiles {
         module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'
@@ -39,6 +61,7 @@ profiles {
         module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/rsem/indexing.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: index_fasta {
         container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "rsem/1.3.0:samtools/1.7"
         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/rsem/indexing.nf

@@ -14,7 +14,6 @@ Channel
 
 process index_fasta {
   tag "$fasta.baseName"
-  cpus 4
   publishDir "results/mapping/index/", mode: 'copy'
 
   input:

src/nf_modules/rsem/quantification_paired.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: mapping_fastq {
         container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "rsem/1.3.0:samtools/1.7"
         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/rsem/quantification_paired.nf

@@ -15,7 +15,6 @@ Channel
 
 process mapping_fastq {
   tag "$pair_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:

src/nf_modules/rsem/quantification_single.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: mapping_fastq {
         container = "rsem:1.3.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "file://bin/rsem:1.3.0.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "rsem/1.3.0:samtools/1.7"
         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/rsem/quantification_single.nf

@@ -20,7 +20,6 @@ Channel
 
 process mapping_fastq {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/quantification/", mode: 'copy'
 
   input:

src/nf_modules/rsem/tests.sh

@@ -19,3 +19,26 @@
   --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
   -resume
 
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/rsem/indexing.nf \
+  -c src/nf_modules/rsem/indexing.config \
+  -profile docker \
+  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+  --annotation "data/tiny_dataset/annot/tiny.gff" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_single.nf \
+  -c src/nf_modules/rsem/quantification_single.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/rsem/quantification_paired.nf \
+  -c src/nf_modules/rsem/quantification_paired.config \
+  -profile docker \
+  --index "results/mapping/index/tiny_v2.index*" \
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
+fi