cutadapt: add singularity to nf files and add -resume to all tests.sh

src/nf_modules/bedtools/fasta_from_bed.nf

@@ -23,7 +23,6 @@ Channel
 
 process fasta_from_bed {
   tag "${bed.baseName}"
-  cpus 4
   publishDir "results/fasta/", mode: 'copy'
 
   input:

src/nf_modules/bowtie/tests.sh

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

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: adaptor_removal {
         container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "cutadapt/1.14"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: adaptor_removal {
         container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "cutadapt/1.14"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/cutadapt/tests.sh

 ./nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
   -c src/nf_modules/cutadapt/adaptor_removal_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/cutadapt/adaptor_removal_single.nf \
   -c src/nf_modules/cutadapt/adaptor_removal_single.config \
   -profile docker \
-  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
 
 ./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
   -c src/nf_modules/cutadapt/trimming_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/cutadapt/trimming_single.nf \
   -c src/nf_modules/cutadapt/trimming_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/cutadapt/adaptor_removal_paired.nf \
+  -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
+  -c src/nf_modules/cutadapt/adaptor_removal_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_paired.nf \
+  -c src/nf_modules/cutadapt/trimming_paired.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq" \
+  -resume
+
+./nextflow src/nf_modules/cutadapt/trimming_single.nf \
+  -c src/nf_modules/cutadapt/trimming_single.config \
+  -profile docker \
+  --fastq "data/tiny_dataset/fastq/tiny*_S.fastq" \
+  -resume
+fi

src/nf_modules/cutadapt/trimming_paired.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: trimming {
         container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "cutadapt/1.14"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/cutadapt/trimming_single.config

@@ -5,6 +5,16 @@ profiles {
     process {
       withName: trimming {
         container = "cutadapt:1.15"
+        cpus = 1
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: trimming {
+        container = "file://bin/cutadapt:1.15.sif"
+        cpus = 1
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "cutadapt/1.14"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 1
         memory = "20GB"
         time = "12h"
         queue = 'monointeldeb128'

src/nf_modules/deeptools/tests.sh

 #!/bin/sh
 
-cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_bis.sort.bam
+cp data/tiny_dataset/map/tiny_v2.sort.bam \
+  data/tiny_dataset/map/tiny_v2_bis.sort.bam
 
-./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf -c src/nf_modules/deeptools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2*.sort.bam"
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+  -c src/nf_modules/deeptools/bam_to_bigwig.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+  -resume
 
-./nextflow src/nf_modules/deeptools/compute_matrix.nf -c src/nf_modules/deeptools/compute_matrix.config -profile docker --bw "results/mapping/bigwig/*.bw" --bed "data/tiny_dataset/annot/tiny.bed"
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+  -c src/nf_modules/deeptools/compute_matrix.config \
+  -profile docker \
+  --bw "results/mapping/bigwig/*.bw" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
 
-./nextflow src/nf_modules/deeptools/plot_profile.nf -c src/nf_modules/deeptools/plot_profile.config -profile docker --matrix "results/mapping/region_matrix/*.mat.gz" --title "plot title"
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+  -c src/nf_modules/deeptools/plot_profile.config \
+  -profile docker \
+  --matrix "results/mapping/region_matrix/*.mat.gz" \
+  --title "plot title" \
+  -resume

src/nf_modules/htseq/tests.sh

@@ -2,5 +2,6 @@
   -c src/nf_modules/htseq/htseq.config \
   -profile docker \
   --gtf "data/tiny_dataset/annot/tiny.gff" \
-  --bam "data/tiny_dataset/map/tiny_v2.bam"
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume
 

src/nf_modules/kallisto/tests.sh

 ./nextflow src/nf_modules/kallisto/indexing.nf \
   -c src/nf_modules/kallisto/indexing.config \
   -profile docker \
-  --fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
+  --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"
+  --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"
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
 

src/nf_modules/multiqc/tests.sh

 ./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"
+  --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"
+  --fastq "data/tiny_dataset/fastq/tiny_S.fastq" \
+  -resume

src/nf_modules/music/tests.sh

@@ -5,4 +5,5 @@ cp results/training/bams/sBNLN18.bam results/training/bams/sBNLN18_control.bam
   --fasta "results/training/fasta/*.fasta" \
   --bam "results/training/bams/s*.bam" \
   --index "results/training/mapping/index/*" \
-  --read_size 50 --frag_size 300
+  --read_size 50 --frag_size 300 \
+  -resume

src/nf_modules/rsem/tests.sh

@@ -2,17 +2,20 @@
   -c src/nf_modules/rsem/indexing.config \
   -profile docker \
   --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
-  --annotation "data/tiny_dataset/annot/tiny.gff"
+  --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"
+  --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"
+  --fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq" \
+  -resume
 

src/nf_modules/samblaster/tests.sh

 ./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"
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  -resume

src/nf_modules/samtools/tests.sh

 ./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"
+  --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"
+  --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"
+  --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"
+  --bed "data/tiny_dataset/OLD/2genes.bed" \
+  -resume

src/nf_modules/sratoolkit/tests.sh

 ./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"
+  --list_srr "src/nf_modules/sratoolkit/list-srr.txt" \
+  -resume