HISAT2:2.0.0: add docker files

src/Rnaseq.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'
-      }
-    }
-  }
-}
-
-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'
-      }
-    }
-  }
-}
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $fasta_from_bed {
-        container = "bedtools:2.25.0"
-      }
-    }
-  }
-  sge {
-    process{
-      $fasta_from_bed {
-        beforeScript = "module purge; module load BEDtools/2.25.0"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
-
-profiles {
-  docker {
-    docker.temp = 'auto'
-    docker.enabled = true
-    process {
-      $index_fasta {
-        container = "kallisto:0.43.1"
-      }
-      $mapping_fastq {
-        container = "kallisto:0.43.1"
-      }
-    }
-  }
-  sge {
-    process{
-      $index_fasta {
-        beforeScript = "module purge; module load Kallisto/0.43.1"
-        executor = "sge"
-        cpus = 1
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-      $mapping_fastq {
-        beforeScript = "module purge; module load Kallisto/0.43.1"
-        executor = "sge"
-        cpus = 4
-        memory = "5GB"
-        time = "6h"
-        queueSize = 1000
-        pollInterval = '60sec'
-        queue = 'h6-E5-2667v4deb128'
-        penv = 'openmp8'
-      }
-    }
-  }
-}
-

src/Rnaseq.nf

-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-params.fasta = "$baseDir/data/fasta/*.fasta"
-params.bed = "$baseDir/data/annot/*.bed"
-
-log.info "fasta file : ${params.fasta}"
-log.info "bed file : ${params.bed}"
-log.info "fastq files : ${params.fastq}"
-
-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 }
-
-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:
-  file "*_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:
-  file reads from fastq_files_cut
-
-  output:
-  file "*_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 ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
-> ${reads[0].baseName}_trimming_report.txt
-"""
-}
-
-process fasta_from_bed {
-  tag "${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"
-  publishDir "results/mapping/index/", mode: 'copy'
-
-  input:
-    file fasta from fasta_files_extracted
-
-  output:
-    file "*.index*" into index_files
-
-  script:
-"""
-kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
-> ${fasta.baseName}_kallisto_report.txt
-"""
-}
-
-
-process mapping_fastq {
-  tag "$reads"
-  cpus 4
-  publishDir "results/mapping/quantification/", mode: 'copy'
-
-  input:
-  file reads from fastq_files_trim
-  file index from index_files
-
-  output:
-  file "*" into counts_files
-
-  script:
-"""
-mkdir ${reads[0].baseName}
-kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
-"""
-}
-
-
-
-

src/fasta_sampler.nf

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