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#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/umi_tools:1.0.0
# docker build src/.docker_modules/umi_tools/1.0.0/ -t 'lbmc/umi_tools:1.0.0'
# docker push lbmc/umi_tools:1.0.0
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/umi_tools:1.0.0" --push src/.docker_modules/umi_tools/1.0.0
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV PACKAGES git=1:2.17.0* \
ENV URQT_VERSION=d62c1f8
ENV PACKAGES git=1:2.17* \
build-essential=12.4* \
ca-certificates=20180409 \
procps \
zlib1g-dev=1:1.2.11*
RUN apt-get update && \
......
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/urqt:d62c1f8
# docker build src/.docker_modules/urqt/d62c1f8 -t 'lbmc/urqt:d62c1f8'
# docker push lbmc/urqt:d62c1f8
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/urqt:d62c1f8" --push src/.docker_modules/urqt/d62c1f8
/sps/lbmc/common/singularity/
\ No newline at end of file
/Xnfs/abc/singularity/
\ No newline at end of file
#!/bin/sh
docker build src/nf_modules/BEDtools/2.25.0 -t 'bedtools:2.25.0'
#!/bin/sh
docker build src/nf_modules/Bowtie2/2.3.4.1 -t 'bowtie2:2.3.4.1'
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$index_fasta {
container = "bowtie2:2.3.4.1"
}
$mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
sge {
process{
$index_fasta {
beforeScript = "module purge; module load Bowtie2/2.3.4.1"
}
$mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
}
}
}
/*
* Bowtie2 :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
*/
/* fasta indexing */
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
.set { fasta_file }
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
output:
file "*.index*" into index_files
script:
"""
bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$pair_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
exit 1
fi
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
.set { fasta_file }
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
output:
file "*.index*" into index_files
script:
"""
bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
params.index = "$baseDir/data/index/*.index.*"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$pair_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index[0].baseName} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
exit 1
fi
"""
}
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
Channel
.fromPath( params.index )
.ifEmpty { error "Cannot find any index files matching: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads.baseName"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*.bam" into bam_files
script:
"""
bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
exit 1
fi
"""
}
nextflow src/nf_modules/Bowtie2/tests/index.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
nextflow src/nf_modules/Bowtie2/tests/mapping_single.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/Bowtie2/tests/mapping_paired.nf \
-c src/nf_modules/Bowtie2/bowtie2.config \
-profile docker \
--index "data/tiny_dataset/fasta/*.bt2" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
#!/bin/sh
docker build src/nf_modules/FastQC/0.11.5 -t 'fastqc:0.11.5'
#!/bin/sh
docker build src/nf_modules/HTSeq/0.8.0 -t 'htseq:0.8.0'
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$counting {
container = "htseq:0.8.0"
}
}
}
sge {
process{
$trimming {
beforeScript = "module purge; module load HTSeq/0.8.0"
}
}
}
}
/*
* htseq :
* Imputs : sorted bams files
* Imputs : gtf
* Output : counts files
*/
/* quality trimming */
params.bam = "$baseDir/data/bam/*.bam"
params.gtf = "$baseDir/data/annotation/*.gtf"
log.info "bam files : ${params.bam}"
log.info "gtf files : ${params.gtf}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
.set { bam_files }
Channel
.fromPath( params.gtf )
.ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
.set { gtf_file }
process counting {
tag "$bam.baseName"
publishDir "results/quantification/", mode: 'copy'
input:
file bam from bam_files
file gtf from gtf_file
output:
file "*.count" into count_files
script:
"""
htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
--format=bam ${bam} ${gtf} > ${bam.baseName}.count
"""
}
params.bam = "$baseDir/data/bam/*.bam"
params.gtf = "$baseDir/data/annotation/*.gtf"
log.info "bam files : ${params.bam}"
log.info "gtf files : ${params.gtf}"
Channel
.fromPath( params.bam )
.ifEmpty { error "Cannot find any fastq files matching: ${params.bam}" }
.set { bam_files }
Channel
.fromPath( params.gtf )
.ifEmpty { error "Cannot find any gtf file matching: ${params.gtf}" }
.set { gtf_file }
process counting {
tag "$bam.baseName"
publishDir "results/quantification/", mode: 'copy'
input:
file bam from bam_files
file gtf from gtf_file
output:
file "*.count" into count_files
script:
"""
htseq-count -r pos --mode=intersection-nonempty -a 10 -s no -t exon -i gene_id \
--format=bam ${bam} ${gtf} > ${bam.baseName}.count
"""
}
nextflow src/nf_modules/HTSeq/tests/counting.nf \
-c src/nf_modules/HTSeq/htseq.config \
-profile docker \
--gtf "data/tiny_dataset/annot/tiny.gff" \
--bam "data/tiny_dataset/map/tiny_v2.bam"
#!/bin/sh
docker build src/nf_modules/Kallisto/0.43.1 -t 'kallisto:0.43.1'