Cutadapt: update nf structure

src/nf_modules/cutadapt/cutadapt.config → src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -24,30 +24,3 @@ profiles {
     }
   }
 }
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $trimming {
-        container = "cutadapt:1.14"
-      }
-    }
-  }
-  sge {
-    process{
-      $trimming {
-        beforeScript = "module purge; module load cutadapt/1.14"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}

src/nf_modules/cutadapt/adaptor_removal_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $adaptor_removal {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  sge {
+    process{
+      $adaptor_removal {
+        beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}

src/nf_modules/cutadapt/cutadapt.nf

-/*
-* cutadapt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-
-/*                      Illumina adaptor removal                             */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process adaptor_removal {
-  tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-  set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
-
-  script:
-  """
-  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
-  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
-  """
-}
-
-/*
-* for single-end data
-*/
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-
-process adaptor_removal {
-  tag "$file_id"
-
-  input:
-  set file_id, file(reads) from fastq_files
-
-  output:
-  set file_id, "*_cut.fastq.gz" into fastq_files_cut
-
-  script:
-  """
-  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
-  -o ${file_id}_cut.fastq.gz \
-  ${reads} > ${file_id}_report.txt
-  """
-}
-
-
-/*                      quality trimming                                     */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromFilePairs( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "$pair_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
-  script:
-  """
-  cutadapt -q 20,20 \
-  -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
-  """
-}
-
-/*
-* for single-end data
-*/
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
-  .fromPath( params.fastq )
-  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
-  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { fastq_files }
-
-process trimming {
-  tag "$file_id"
-
-  input:
-  set file_id, file(reads) from fastq_files
-
-  output:
-  set file_id, "*_trim.fastq.gz" into fastq_files_cut
-
-  script:
-  """
-  cutadapt -q 20,20 \
-  -o ${file_id}_trim.fastq.gz \
-  ${reads} > ${file_id}_report.txt
-  """
-}
-

src/nf_modules/cutadapt/tests/tests.sh → src/nf_modules/cutadapt/tests.sh

-nextflow src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf \
-  -c src/nf_modules/cutadapt/cutadapt.config \
+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"
 
-nextflow src/nf_modules/cutadapt/tests/adaptor_removal_single.nf \
-  -c src/nf_modules/cutadapt/cutadapt.config \
+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"
 
-nextflow src/nf_modules/cutadapt/tests/trimming_paired.nf \
-  -c src/nf_modules/cutadapt/cutadapt.config \
+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"
 
-nextflow src/nf_modules/cutadapt/tests/trimming_single.nf \
-  -c src/nf_modules/cutadapt/cutadapt.config \
+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"

src/nf_modules/cutadapt/trimming_paired.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $trimming {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}

src/nf_modules/cutadapt/trimming_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $trimming {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load cutadapt/1.14"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}