Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found
Select Git revision
  • dev
  • master
  • v0.1.0
  • v0.1.2
  • v0.2.0
  • v0.2.1
  • v0.2.2
  • v0.2.3
  • v0.2.4
  • v0.2.5
  • v0.2.6
  • v0.2.7
  • v0.2.8
  • v0.2.9
  • v0.3.0
  • v0.4.0
  • v2.0.0
17 results

Target

Select target project
  • LBMC/regards/nextflow
  • elabaron/nextflow
  • lanani/nextflow
  • mlepetit/nextflow
  • mdjaffar/nextflow
  • LBMC/RMI2/rmi2_pipelines
  • lpicard/nextflow
  • rseraphi/nextflow
  • hregue/nextflow
  • letien02/nextflow
  • mshamjal/nextflow
  • z483801/nextflow
  • fduveau/nextflow
  • cginevra/nextflow
  • dtorresc/nextflow
  • fmortreu/nextflow
  • jshapiro/nextflow
  • carpin/nextflow
  • LBMC/Delattre/JU28_59vs17_SNP
  • jclaud01/nextflow
  • dchalopi/nextflow
  • mvilcot/nextflow
  • mherbett/nextflow
  • lestrada/nextflow
  • nfontrod/nextflow
  • gbenoit/nextflow
  • gyvert/nextflow
  • aguill09/nextflow
  • alapendr/nextflow
  • jprobin/nextflow
  • vvanoost/nextflow
  • jblin/nextflow
  • mparis/nextflow
  • ogandril/nextflow
  • cbourgeo/nextflow
  • ggirau03/nextflow
  • ecombe01/nextflow
  • acorbin/nextflow
  • pberna01/nextflow
  • pmarie01/nextflow
  • rhoury/nextflow
  • lgely/nextflow
  • jvalat/nextflow
  • cfournea/nextflow
  • mprieux/nextflow
  • hpolvech/nextflow
  • LBMC/nextflow
  • mcariou/nextflow
  • z483800/nextflow
  • yjia01/nextflow
  • jkleine/nextflow
  • LBMC/Palladino/RNAseq_nextflow
  • jseimand/nextflow
  • nlecouvr/nextflow-nathan
54 results
Select Git revision
  • dev
  • master
  • v0.1.0
  • v0.1.2
  • v0.2.0
  • v0.2.1
  • v0.2.2
  • v0.2.3
  • v0.2.4
  • v0.2.5
  • v0.2.6
  • v0.2.7
  • v0.2.8
  • v0.2.9
14 results
Show changes
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
BOWTIE2_VERSION=2.3.4.1
SAMTOOLS_VERSION=1.7
PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
samtools=${SAMTOOLS_VERSION}* \
perl=5.26.1*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export BOWTIE2_VERSION=2.3.4.1
export SAMTOOLS_VERSION=1.7
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/Bowtie2/2.3.4.1/Bowtie2.def
singularity sign bin/bowtie2:2.3.4.1.sif
Bootstrap: library
From: debian:9
%labels
MAINTAINER Laurent Modolo
%post
URQT_VERSION=d62c1f8
PACKAGES="git \
g++ \
make \
ca-certificates \
zlib1g-dev"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
git clone https://github.com/l-modolo/UrQt.git && \
cd UrQt && \
git checkout ${URQT_VERSION} && \
make && \
cd .. && \
mv UrQt/UrQt /usr/bin/ && \
rm -Rf UrQt
%environment
export URQT_VERSION=d62c1f8
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/UrQt:d62c1f8.sif src/singularity_modules/UrQt/d62c1f8/UrQt.def
singularity sign bin/UrQt:d62c1f8.sif
#/bin/sh
sudo singularity build --force bin/fastqc:0.11.5.sif src/singularity_modules/fastqc/0.11.5/fastqc.def
singularity sign bin/fastqc:0.11.5.sif
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
FASTQC_VERSION=0.11.5
PACKAGES="fastqc=${FASTQC_VERSION}* \
perl=5.26*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
%environment
export FASTQC_VERSION=0.11.5
export PACKAGES=fastqc=${FASTQC_VERSION}*
%runscript
exec /bin/bash "$@"
#/bin/sh
sudo singularity build --force bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def
singularity sign bin/sambamba:0.6.7.sif
Bootstrap: docker
From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
%post
SAMBAMBA_VERSION=0.6.7
PACKAGES="curl=7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*"
apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
mv sambamba /usr/bin/ && \
rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
%environment
export SAMBAMBA_VERSION=0.6.7
%runscript
exec /bin/bash "$@"
// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
//
// SPDX-License-Identifier: AGPL-3.0-or-later
nextflow.enable.dsl=2
include { fastp } from "./nf_modules/fastp/main.nf"
include { fasta_from_bed } from "./nf_modules/bedtools/main.nf"
include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf' addParams(mapping_fastq_out: "quantification/")
params.fastq = "data/fastq/*_{1,2}.fastq"
log.info "fastq files: ${params.fastq}"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
channel
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.map { it -> [it.simpleName, it]}
.set { fasta_files }
channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.map { it -> [it.simpleName, it]}
.set { bed_files }
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
index_fasta(fasta_from_bed.out.fasta)
mapping_fastq(index_fasta.out.index.collect(), fastp.out.fastq)
}
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
profiles {
docker {
docker.temp = 'auto'
docker.temp = "auto"
docker.enabled = true
process {
withname: build_synthetic_bed {
container = "bedtools:2.25.0"
withName: build_synthetic_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withname: fasta_from_bed {
container = "bedtools:2.25.0"
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withname: index_fasta {
container = "bowtie2:2.3.4.1"
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withname: mapping_fastq_paired {
container = "bowtie2:2.3.4.1"
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withname: bam_2_fastq_paired {
container = "samtools:1.7"
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withname: sort_bam_paired {
container = "samtools:1.7"
withName: filter_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withname: index_bam_paired {
container = "samtools:1.7"
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withname: mapping_fastq_single {
container = "bowtie2:2.3.4.1"
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withname: bam_2_fastq_single {
container = "samtools:1.7"
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withname: sort_bam_single {
container = "samtools:1.7"
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withname: index_bam_single {
container = "samtools:1.7"
withName: filter_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
}
}
singularity {
singularity.enabled = true
singularity.cacheDir = "./bin/"
process {
withName: build_synthetic_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
cpus = 1
}
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_single {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
withName: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_paired {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: filter_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: sort_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
withName: index_bam_single {
container = "lbmc/samtools:1.7"
cpus = 4
}
}
}
psmn {
process{
withname: build_synthetic_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BEDtools/2.25.0"
withName: build_synthetic_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m be -cwd -V"
clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
queue = "monointeldeb128"
}
withname: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "BEDtools/2.25.0"
withName: fasta_from_bed {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m be -cwd -V"
clusterOptions = "-m e -cwd -V"
cpus = 1
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
queue = "monointeldeb128"
}
withname: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1"
withName: index_fasta {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "20GB"
time = "12h"
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withName: mapping_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: mapping_fastq_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
withName: bam_2_fastq_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: bam_2_fastq_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
withName: sort_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: sort_bam_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
withName: index_bam_paired {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: index_bam_paired {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
withName: mapping_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
clusterOptions = "-m e -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_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "Bowtie2/2.3.4.1:SAMtools/1.7"
withName: bam_2_fastq_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
penv = 'openmp16'
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: bam_2_fastq_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
withName: sort_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
clusterOptions = "-m e -cwd -V"
cpus = 32
memory = "30GB"
time = "24h"
queue = "CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D"
penv = "openmp32"
}
withname: sort_bam_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
withName: index_bam_single {
beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
clusterOptions = "-m e -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: 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_bam_single {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "SAMtools/1.7"
process{
withName: build_synthetic_bed {
container = "lbmc/bedtools:2.25.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
memory = "20GB"
time = "12h"
queue = 'monointeldeb128'
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/bowtie2:2.3.4.1"
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: mapping_fastq_paired {
container = "lbmc/bowtie2:2.3.4.1"
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: bam_2_fastq_paired {
container = "lbmc/samtools:1.7"
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: sort_bam_paired {
container = "lbmc/samtools:1.7"
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_bam_paired {
container = "lbmc/samtools:1.7"
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_single {
container = "lbmc/bowtie2:2.3.4.1"
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: bam_2_fastq_single {
container = "lbmc/samtools:1.7"
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: sort_bam_single {
container = "lbmc/samtools:1.7"
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_bam_single {
container = "lbmc/samtools:1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = "huge"
}
}
}
......
// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
//
// SPDX-License-Identifier: AGPL-3.0-or-later
/*
small pipeline to build a training dataset from whole genome data
......