Merge branch 'dev'

src/nf_modules/SAMtools/sort_bams.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $sort_bam {
+        container = "samtools:1.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $sort_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+    }
+  }
+}

src/nf_modules/SAMtools/tests/sort_bams.nf → src/nf_modules/SAMtools/sort_bams.nf

@@ -5,21 +5,22 @@ log.info "bams files : ${params.bam}"
 Channel
   .fromPath( params.bam )
   .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set { bam_files }
 
 process sort_bam {
-  tag "$bams.baseName"
+  tag "$file_id"
   cpus 4
 
   input:
-    file bam from bam_files
+    set file_id, file(bam) from bam_files
 
   output:
-    file "*_sorted.bam" into sorted_bam_files
+    set file_id, "*_sorted.bam" into sorted_bam_files
 
   script:
 """
-samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
+samtools sort -@ ${task.cpus} -O BAM -o ${file_id}_sorted.bam ${bam}
 """
 }
 

src/nf_modules/SAMtools/split_bams.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $split_bam {
+        container = "samtools:1.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $split_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+    }
+  }
+}

src/nf_modules/SAMtools/tests/split_bams.nf → src/nf_modules/SAMtools/split_bams.nf

@@ -5,22 +5,23 @@ log.info "bams files : ${params.bam}"
 Channel
   .fromPath( params.bam )
   .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set { bam_files }
 
 process split_bam {
-  tag "$bam.baseName"
+  tag "$file_id"
   cpus 2
 
   input:
-    file bam from bam_files
+    set file_id, file(bam) from bam_files
 
   output:
-    file "*_forward.bam*" into forward_bam_files
-    file "*_reverse.bam*" into reverse_bam_files
+    set file_id, "*_forward.bam*" into forward_bam_files
+    set file_id, "*_reverse.bam*" into reverse_bam_files
   script:
 """
-samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
+samtools view -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
 """
 }
 

src/nf_modules/SAMtools/tests/tests.sh → src/nf_modules/SAMtools/tests.sh

-nextflow src/nf_modules/SAMtools/tests/sort_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
+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"
 
-nextflow src/nf_modules/SAMtools/tests/index_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
+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"
 
-nextflow src/nf_modules/SAMtools/tests/split_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
+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"
 
-nextflow src/nf_modules/SAMtools/tests/filter_bams.nf \
-  -c src/nf_modules/SAMtools/samtools.config \
+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"

src/nf_modules/SRAtoolkit/tests/fastqdump.nf → src/nf_modules/SRAtoolkit/fastqdump.nf

@@ -15,30 +15,33 @@ log.info "downloading list srr : ${params.list_srr}"
 Channel
   .fromPath( params.list_srr )
   .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
-  .splitCsv(header: true)
+  .splitCsv()
+  .map { it -> it[0]}
   .set { SRR }
 
 //run is the column name containing SRR ids
 
 process fastq_dump {
-  tag {"${x.run}"}
-  publishDir "results/download/fastq/${x.run}/", mode: 'copy'
+  tag "$file_id"
+  publishDir "results/download/fastq/${file_id}/", mode: 'copy'
 
   input:
-    val x  from SRR
+    val file_id from SRR
 
   output:
-    file("*") into fastq
+    set file_id, "*.fastq" into fastq
 
   script:
 """
 #for test only 10000  reads are downloading with the option -N 10000 -X 20000
-fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${x.run}
-if [ -f ${x.run}_1.fastq ]
+fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${file_id}
+if [ -f ${file_id}_1.fastq ]
 then
-  true
-else
-  touch ${x.run}.fastq
+  mv ${file_id}_1.fastq ${file_id}_R1.fastq
+fi
+if [ -f ${file_id}_2.fastq ]
+then
+  mv ${file_id}_2.fastq ${file_id}_R2.fastq
 fi
 """
 }

src/nf_modules/SRAtoolkit/tests/list-srr.txt → src/nf_modules/SRAtoolkit/list-srr.txt

-run
 ERR572281
 ERR572146
 ERR572201

src/nf_modules/SRAtoolkit/sratoolkit.nf

-/*
-* sra-tools :
-
-*/
-
-/*                      fastq-dump
-* Imputs : srr list
-* Outputs : fastq files
-*/
-
-params.list_srr = "$baseDir/data/SRR/*.txt"
-
-log.info "downloading list srr : ${params.list_srr}"
-
-Channel
-  .fromPath( params.list_srr )
-  .ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
-  .splitCsv(header: true)
-  .set { SRR }
-
-//run is the column name containing SRR ids
-
-process fastq_dump {
-  tag {"${x.run}"}
-  publishDir "results/download/fastq/${x.run}/", mode: 'copy'
-
-  input:
-    val x  from SRR
-
-  output:
-    file("*") into fastq
-
-  script:
-"""
-fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+"  ${x.run}
-if [ -f ${x.run}_1.fastq ]
-then
-  true
-else
-  touch ${x.run}.fastq
-fi
-"""
-}

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"

src/nf_modules/SRAtoolkit/tests/tests.sh

-nextflow src/nf_modules/SRAtoolkit/tests/fastqdump.nf \
-  -c src/nf_modules/SRAtoolkit/sratoolkit.config \
-  -profile docker \
-  --list_srr "src/nf_modules/SRAtoolkit/tests/list-srr.txt"

src/nf_modules/UrQt/tests/tests.sh → src/nf_modules/UrQt/tests.sh

-nextflow src/nf_modules/UrQt/tests/trimming_paired.nf \
-  -c src/nf_modules/UrQt/urqt.config \
+nextflow src/nf_modules/UrQt/trimming_paired.nf \
+  -c src/nf_modules/UrQt/trimming_paired.config \
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
 
-nextflow src/nf_modules/UrQt/tests/trimming_single.nf \
-  -c src/nf_modules/UrQt/urqt.config \
+nextflow src/nf_modules/UrQt/trimming_single.nf \
+  -c src/nf_modules/UrQt/trimming_single.config \
   -profile docker \
   --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"

src/nf_modules/UrQt/trimming_paired.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $trimming {
+        container = "urqt:d62c1f8"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load UrQt/d62c1f8"
+        executor = "sge"
+        cpus = 4
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}

src/nf_modules/UrQt/trimming_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $trimming {
+        container = "urqt:d62c1f8"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load UrQt/d62c1f8"
+        executor = "sge"
+        cpus = 4
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}

src/nf_modules/UrQt/urqt.nf

-/*
-* urqt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-/*                      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: ${params.fastq}" }
-  .set { fastq_files }
-
-process trimming {
-  tag "${reads}"
-  cpus 4
-  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:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads[0]} --inpair ${reads[1]} \
---out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
-> ${pair_id}_trimming_report.txt
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-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"
-  cpus 4
-
-  input:
-  set file_id, file(reads) from fastq_files
-
-  output:
-  set file_id, "*_trim.fastq.gz" into fastq_files_trim
-
-  script:
-  """
-  UrQt --t 20 --m ${task.cpus} --gz \
-  --in ${reads} \
-  --out ${file_id}_trim.fastq.gz \
-  > ${file_id}_trimming_report.txt
-  """
-}

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'
+      }
+    }
+  }
+}