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Unverified Commit ffb23d50 authored by Laurent Modolo's avatar Laurent Modolo
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training_dataset.config: update config to match latest changes

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src/training_dataset.config
+ 49
− 48
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...@@ -4,112 +4,113 @@ profiles { ...@@ -4,112 +4,113 @@ profiles {
docker.enabled = true docker.enabled = true
process { process {
withName: build_synthetic_bed { withName: build_synthetic_bed {
container = "bedtools:2.25.0" container = "lbmc/bedtools:2.25.0"
cpus = 1 cpus = 1
} }
withName: fasta_from_bed { withName: fasta_from_bed {
container = "bedtools:2.25.0" container = "lbmc/bedtools:2.25.0"
cpus = 1 cpus = 1
} }
withName: index_fasta { withName: index_fasta {
container = "bowtie2:2.3.4.1" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: mapping_fastq_paired { withName: mapping_fastq_paired {
container = "bowtie2:2.3.4.1" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: bam_2_fastq_paired { withName: bam_2_fastq_paired {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: filter_bam_paired { withName: filter_bam_paired {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: sort_bam_paired { withName: sort_bam_paired {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: index_bam_paired { withName: index_bam_paired {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: mapping_fastq_single { withName: mapping_fastq_single {
container = "bowtie2:2.3.4.1" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: bam_2_fastq_single { withName: bam_2_fastq_single {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: filter_bam_single { withName: filter_bam_single {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: sort_bam_single { withName: sort_bam_single {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: index_bam_single { withName: index_bam_single {
container = "samtools:1.7" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
} }
} }
singularity { singularity {
singularity.enabled = true singularity.enabled = true
singularity.cacheDir = "./bin/"
process { process {
withName: build_synthetic_bed { withName: build_synthetic_bed {
container = "file://bin/bedtools:2.25.0.img" container = "lbmc/bedtools:2.25.0"
cpus = 1 cpus = 1
} }
withName: fasta_from_bed { withName: fasta_from_bed {
container = "file://bin/bedtools:2.25.0.img" container = "lbmc/bedtools:2.25.0"
cpus = 1 cpus = 1
} }
withName: index_fasta { withName: index_fasta {
container = "file://bin/bowtie2:2.3.4.1.img" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: mapping_fastq_single { withName: mapping_fastq_single {
container = "file://bin/bowtie2:2.3.4.1.img" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: mapping_fastq_paired { withName: mapping_fastq_paired {
container = "file://bin/bowtie2:2.3.4.1.img" container = "lbmc/bowtie2:2.3.4.1"
cpus = 4 cpus = 4
} }
withName: bam_2_fastq_paired { withName: bam_2_fastq_paired {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: filter_bam_paired { withName: filter_bam_paired {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: sort_bam_paired { withName: sort_bam_paired {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: index_bam_paired { withName: index_bam_paired {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: bam_2_fastq_single { withName: bam_2_fastq_single {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: filter_bam_single { withName: filter_bam_single {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: sort_bam_single { withName: sort_bam_single {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
withName: index_bam_single { withName: index_bam_single {
container = "file://bin/samtools:1.7.img" container = "lbmc/samtools:1.7"
cpus = 4 cpus = 4
} }
} }
...@@ -117,8 +118,8 @@ profiles { ...@@ -117,8 +118,8 @@ profiles {
psmn { psmn {
process{ process{
withName: build_synthetic_bed { withName: build_synthetic_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "bedtools/2.25.0" conda = "${CONDA_ENVS}bedtools_2.25.0"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1 cpus = 1
...@@ -127,8 +128,8 @@ profiles { ...@@ -127,8 +128,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
} }
withName: fasta_from_bed { withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "bedtools/2.25.0" conda = "${CONDA_ENVS}bedtools_2.25.0"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 1 cpus = 1
...@@ -137,8 +138,8 @@ profiles { ...@@ -137,8 +138,8 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128' queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
} }
withName: index_fasta { withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "bowtie2/2.3.4.1" conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -148,8 +149,8 @@ profiles { ...@@ -148,8 +149,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: mapping_fastq_paired { withName: mapping_fastq_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "bowtie2/2.3.4.1:samtools/1.7" conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -159,8 +160,8 @@ profiles { ...@@ -159,8 +160,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: bam_2_fastq_paired { withName: bam_2_fastq_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -170,8 +171,8 @@ profiles { ...@@ -170,8 +171,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: sort_bam_paired { withName: sort_bam_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -181,8 +182,8 @@ profiles { ...@@ -181,8 +182,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: index_bam_paired { withName: index_bam_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -192,8 +193,8 @@ profiles { ...@@ -192,8 +193,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: mapping_fastq_single { withName: mapping_fastq_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "bowtie2/2.3.4.1:samtools/1.7" conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -203,8 +204,8 @@ profiles { ...@@ -203,8 +204,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: bam_2_fastq_single { withName: bam_2_fastq_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -214,8 +215,8 @@ profiles { ...@@ -214,8 +215,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: sort_bam_single { withName: sort_bam_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
...@@ -225,8 +226,8 @@ profiles { ...@@ -225,8 +226,8 @@ profiles {
penv = 'openmp16' penv = 'openmp16'
} }
withName: index_bam_single { withName: index_bam_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules" beforeScript = "./src/conda_psmn.sh"
module = "samtools/1.7" conda = "${CONDA_ENVS}samtools_1.7"
executor = "sge" executor = "sge"
clusterOptions = "-m e -cwd -V" clusterOptions = "-m e -cwd -V"
cpus = 16 cpus = 16
......
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