t Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/nextflow

 the commit.

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
+"""
+}

src/solution_RNASeq.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.1"
+        cpus = 1
+      }
+      withName: trimming {
+        cpus = 4
+        container = "lbmc/urqt:d62c1f8"
+      }
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        cpus = 1
+      }
+      withName: index_fasta {
+        container = "lbmc/kallisto:0.44.0"
+        cpus = 4
+      }
+      withName: mapping_fastq {
+        container = "lbmc/kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    singularity.cacheDir = "./bin/"
+    process {
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.1"
+        cpus = 1
+      }
+      withName: trimming {
+        cpus = 4
+        container = "lbmc/urqt:d62c1f8"
+      }
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        cpus = 1
+      }
+      withName: index_fasta {
+        container = "lbmc/kallisto:0.44.0"
+        cpus = 4
+      }
+      withName: mapping_fastq {
+        container = "lbmc/kallisto:0.44.0"
+        cpus = 4
+      }
+    }
+  }
+  psmn{
+    process{
+      withName: adaptor_removal {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/cutadapt_2.1"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+      withName: trimming {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/urqt_d62c1f8"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 32
+        memory = "30GB"
+        time = "24h"
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+        penv = 'openmp32'
+
+      }
+      withName: fasta_from_bed {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bedtools_2.25.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128'
+      }
+      withName: index_fasta {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 32
+        memory = "30GB"
+        time = "24h"
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+        penv = 'openmp32'
+      }
+      withName: mapping_fastq {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/kallisto_0.44.0"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 32
+        memory = "30GB"
+        time = "24h"
+        queue = 'CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D'
+        penv = 'openmp32'
+      }
+    }
+  }
+  ccin2p3 {
+    singularity.enabled = true
+    singularity.cacheDir = "$baseDir/.singularity_in2p3/"
+    singularity.runOptions = "--bind /pbs,/sps,/scratch"
+    process{
+      withName: adaptor_removal {
+        container = "lbmc/cutadapt:2.1"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: trimming {
+        container = "lbmc/urqt:d62c1f8"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: fasta_from_bed {
+        container = "lbmc/bedtools:2.25.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: index_fasta {
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+      withName: mapping_fastq {
+        container = "lbmc/kallisto:0.44.0"
+        scratch = true
+        stageInMode = "copy"
+        stageOutMode = "rsync"
+        executor = "sge"
+        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+        "
+        cpus = 1
+        queue = 'huge'
+      }
+    }
+  }
+}

src/solution_RNASeq.nf

+log.info "fastq files : ${params.fastq}"
+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 }
+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}"
+  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 \
+> ${pair_id}_trimming_report.txt
+"""
+}
+
+process fasta_from_bed {
+  tag "${bed.baseName}"
+  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
+    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"
+  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
+"""
+}