src/RNASeq.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "cutadapt:1.14"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: adaptor_removal {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "cutadapt/1.14"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: trimming {
+        container = "urqt:d62c1f8"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: trimming {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "UrQt/d62c1f8"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "5GB"
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: fasta_from_bed {
+        container = "bedtools:2.25.0"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: fasta_from_bed {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "BEDtools/2.25.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+    }
+  }
+}
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        container = "kallisto:0.44.0"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        container = "kallisto:0.44.0"
+      }
+    }
+  }
+  psmn {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+}
+
+

src/RNASeq.nf

+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]} > ${pair_id}_report.txt
+  """
+}
+
+
+
+process trimming {
+  tag "${reads}"
+  cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_cut
+
+  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 \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+
+params.fasta = "$baseDir/data/fasta/*.fasta"
+params.bed = "$baseDir/data/annot/*.bed"
+
+log.info "fasta file : ${params.fasta}"
+log.info "bed file : ${params.bed}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .set { fasta_files }
+Channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+  .set { bed_files }
+
+process fasta_from_bed {
+  tag "${bed.baseName}"
+  cpus 4
+  publishDir "results/fasta/", mode: 'copy'
+
+  input:
+  file fasta from fasta_files
+  file bed from bed_files
+
+  output:
+  file "*_extracted.fasta" into fasta_files_extracted
+
+  script:
+"""
+bedtools getfasta -name \
+-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
+"""
+}
+
+
+process index_fasta {
+  tag "$fasta.baseName"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_files_extracted
+
+  output:
+    file "*.index*" into index_files
+    file "*_kallisto_report.txt" into index_files_report
+
+  script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+2> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+
+
+process mapping_fastq {
+  tag "$reads"
+  cpus 4
+  publishDir "results/mapping/quantification/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_trim
+  file index from index_files.collect()
+
+  output:
+  file "*" into counts_files
+
+  script:
+"""
+mkdir ${pair_id}
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
+"""
+}
+
+

src/fasta_sampler.nf

+Channel
+  .fromPath( "data/tiny_dataset/fasta/*.fasta" )
+  .set { fasta_file }
+
+process sample_fasta {
+  input:
+file fasta from fasta_file
+
+  
+
+publishDir "results/sampling/", mode: 'copy'
+
+output:
+file "*_sample.fasta" into fasta_sample
+
+  script:
+"""
+head ${fasta} > ${fasta.baseName}_sample.fasta
+"""
+
+}