fastqc: add singularity to nf files

src/nf_modules/fastqc/fastqc_paired.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: fastqc_fastq {
         container = "fastqc:0.11.5"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        cpus = 1
+        container = "file://bin/fastqc:0.11.5.sif"
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "FastQC/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/fastqc/fastqc_single.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: fastqc_fastq {
         container = "fastqc:0.11.5"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: fastqc_fastq {
+        cpus = 1
+        container = "file://bin/fastqc:0.11.5.sif"
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "FastQC/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/fastqc/fastqc_single.nf

@@ -11,7 +11,6 @@ Channel
 process fastqc_fastq {
   tag "$file_id"
   publishDir "results/fastq/fastqc/", mode: 'copy'
-  cpus = 1
 
   input:
   set file_id, file(reads) from fastq_files

src/nf_modules/fastqc/tests.sh

 ./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
   -c src/nf_modules/fastqc/fastqc_paired.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
 
 ./nextflow src/nf_modules/fastqc/fastqc_single.nf \
   -c src/nf_modules/fastqc/fastqc_single.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/fastqc/fastqc_paired.nf \
+  -c src/nf_modules/fastqc/fastqc_paired.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/fastqc/fastqc_single.nf \
+  -c src/nf_modules/fastqc/fastqc_single.config \
+  -profile singularity \
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume
+fi

src/nf_modules/urqt/trimming_paired.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: trimming {
         cpus = 4
-        container = "file://bin/UrQt:d62c1f8.sif"
+        container = "file://bin/urqt:d62c1f8.sif"
       }
     }
   }

src/nf_modules/urqt/trimming_single.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: trimming {
-        container = "file://bin/UrQt:d62c1f8.sif"
+        container = "file://bin/urqt:d62c1f8.sif"
         cpus = 4
       }
     }