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Unverified Commit 7fa6b2d4 authored by Laurent Modolo's avatar Laurent Modolo
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fix training_dataset pipeline

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Pipeline #45 canceled
Stage: build
    Stage: test
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      src/nf_modules/bedtools/fasta_from_bed.config
      + 1
      − 0
      View file @ 7fa6b2d4
      ......@@ -25,6 +25,7 @@ profiles {
      module = "bedtools/2.25.0"
      executor = "sge"
      clusterOptions = "-m e -cwd -V"
      cpus = 1
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      ......
      src/training_dataset.config
      + 157
      − 55
      View file @ 7fa6b2d4
      ......@@ -3,135 +3,237 @@ profiles {
      docker.temp = 'auto'
      docker.enabled = true
      process {
      withname: build_synthetic_bed {
      withName: build_synthetic_bed {
      container = "bedtools:2.25.0"
      cpus = 1
      }
      withname: fasta_from_bed {
      withName: fasta_from_bed {
      container = "bedtools:2.25.0"
      cpus = 1
      }
      withname: index_fasta {
      withName: index_fasta {
      container = "bowtie2:2.3.4.1"
      cpus = 4
      }
      withname: mapping_fastq_paired {
      withName: mapping_fastq_paired {
      container = "bowtie2:2.3.4.1"
      cpus = 4
      }
      withname: bam_2_fastq_paired {
      withName: bam_2_fastq_paired {
      container = "samtools:1.7"
      cpus = 4
      }
      withname: sort_bam_paired {
      withName: filter_bam_paired {
      container = "samtools:1.7"
      cpus = 4
      }
      withname: index_bam_paired {
      withName: sort_bam_paired {
      container = "samtools:1.7"
      cpus = 4
      }
      withname: mapping_fastq_single {
      withName: index_bam_paired {
      container = "samtools:1.7"
      cpus = 4
      }
      withName: mapping_fastq_single {
      container = "bowtie2:2.3.4.1"
      cpus = 4
      }
      withname: bam_2_fastq_single {
      withName: bam_2_fastq_single {
      container = "samtools:1.7"
      cpus = 4
      }
      withname: sort_bam_single {
      withName: filter_bam_single {
      container = "samtools:1.7"
      cpus = 4
      }
      withname: index_bam_single {
      withName: sort_bam_single {
      container = "samtools:1.7"
      cpus = 4
      }
      withName: index_bam_single {
      container = "samtools:1.7"
      cpus = 4
      }
      }
      }
      singularity {
      singularity.enabled = true
      process {
      withName: build_synthetic_bed {
      container = "file://bin/bedtools:2.25.0.sif"
      cpus = 1
      }
      withName: fasta_from_bed {
      container = "file://bin/bedtools:2.25.0.sif"
      cpus = 1
      }
      withName: index_fasta {
      container = "file://bin/bowtie2:2.3.4.1.sif"
      cpus = 4
      }
      withName: mapping_fastq_single {
      container = "file://bin/bowtie2:2.3.4.1.sif"
      cpus = 4
      }
      withName: mapping_fastq_paired {
      container = "file://bin/bowtie2:2.3.4.1.sif"
      cpus = 4
      }
      withName: bam_2_fastq_paired {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: filter_bam_paired {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: sort_bam_paired {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: index_bam_paired {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: bam_2_fastq_single {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: filter_bam_single {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: sort_bam_single {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      withName: index_bam_single {
      container = "file://bin/samtools:1.7.sif"
      cpus = 4
      }
      }
      }
      psmn {
      process{
      withname: build_synthetic_bed {
      withName: build_synthetic_bed {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "BEDtools/2.25.0"
      module = "bedtools/2.25.0"
      executor = "sge"
      clusterOptions = "-m be -cwd -V"
      clusterOptions = "-m e -cwd -V"
      cpus = 1
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      }
      withname: fasta_from_bed {
      withName: fasta_from_bed {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "BEDtools/2.25.0"
      module = "bedtools/2.25.0"
      executor = "sge"
      clusterOptions = "-m be -cwd -V"
      clusterOptions = "-m e -cwd -V"
      cpus = 1
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      }
      withname: index_fasta {
      withName: index_fasta {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "Bowtie2/2.3.4.1"
      module = "bowtie2/2.3.4.1"
      executor = "sge"
      memory = "30GB"
      time = "24h"
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "20GB"
      time = "12h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: mapping_fastq_paired {
      withName: mapping_fastq_paired {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "Bowtie2/2.3.4.1:SAMtools/1.7"
      module = "bowtie2/2.3.4.1:samtools/1.7"
      executor = "sge"
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: bam_2_fastq_paired {
      withName: bam_2_fastq_paired {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: sort_bam_paired {
      withName: sort_bam_paired {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: index_bam_paired {
      withName: index_bam_paired {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: mapping_fastq_single {
      withName: mapping_fastq_single {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "Bowtie2/2.3.4.1:SAMtools/1.7"
      module = "bowtie2/2.3.4.1:samtools/1.7"
      executor = "sge"
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: bam_2_fastq_single {
      withName: bam_2_fastq_single {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: sort_bam_single {
      withName: sort_bam_single {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      withname: index_bam_single {
      withName: index_bam_single {
      beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
      module = "SAMtools/1.7"
      module = "samtools/1.7"
      executor = "sge"
      memory = "20GB"
      time = "12h"
      queue = 'monointeldeb128'
      clusterOptions = "-m e -cwd -V"
      cpus = 16
      memory = "30GB"
      time = "24h"
      queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
      penv = 'openmp16'
      }
      }
      }
      ......
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