From 7fa6b2d41b43b79a74d640a1544054c0b0d8ab6b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Mar 2019 17:24:47 +0100
Subject: [PATCH] fix training_dataset pipeline
---
src/nf_modules/bedtools/fasta_from_bed.config | 1 +
src/training_dataset.config | 212 +++++++++++++-----
2 files changed, 158 insertions(+), 55 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 0a70980b..1e1aad47 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -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'
diff --git a/src/training_dataset.config b/src/training_dataset.config
index b416751d..baebb4cf 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -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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