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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:
set pair_id, "*.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"
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"
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$index_fasta {
container = "kallisto:0.44.0"
}
$mapping_fastq {
container = "kallisto:0.44.0"
}
}
}
sge {
process{
$index_fasta {
beforeScript = "module purge; module load Kallisto/0.44.0"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
$mapping_fastq {
beforeScript = "module purge; module load Kallisto/0.44.0"
executor = "sge"
cpus = 4
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
}
}
}
/*
* Kallisto :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
*/
/* fasta indexing */
params.fasta = "$baseDir/data/bam/*.fasta"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_file }
process index_fasta {
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
output:
file "*.index*" into index_files
script:
"""
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
> ${fasta.baseName}_kallisto_report.txt
"""
}
/*
* for paired-end data
*/
params.fastq = "$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: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*" into counts_files
script:
"""
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 200
params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
log.info "mean read size: ${params.mean}"
log.info "sd read size: ${params.sd}"
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/quantification/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*" into count_files
script:
"""
mkdir ${reads.baseName}
kallisto quant -i ${index} -t ${task.cpus} --single
--bias --bootstrap-samples 100 -o ${reads.baseName} \
-l ${params.mean} -s ${params.sd} -o ./ \
${reads} > ${reads.baseName}_kallisto_report.txt
"""
}
params.fasta = "$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:
"""
kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
> ${fasta.baseName}_kallisto_report.txt
"""
}
params.fastq = "$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: ${params.index}" }
.set { index_files }
process mapping_fastq {
tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*" into counts_files
script:
"""
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
"""
}
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 200
params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
log.info "mean read size: ${params.mean}"
log.info "sd read size: ${params.sd}"
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/quantification/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*" into count_files
script:
"""
mkdir ${reads.baseName}
kallisto quant -i ${index} -t ${task.cpus} --single \
--bias --bootstrap-samples 100 -o ${reads.baseName} \
-l ${params.mean} -s ${params.sd} \
${reads} > ${reads.baseName}_kallisto_report.txt
"""
}
nextflow src/nf_modules/Kallisto/tests/index.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta"
nextflow src/nf_modules/Kallisto/tests/mapping_single.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/Kallisto/tests/mapping_paired.nf \
-c src/nf_modules/Kallisto/kallisto.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$index_fasta {
container = "rsem:1.3.0"
}
$mapping_fastq {
container = "rsem:1.3.0"
}
}
}
sge {
process{
$index_fasta {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
$mapping_fastq {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
}
}
}
/*
* RSEM :
* Imputs : fastq files
* Imputs : fasta files
* Output : bam files
*/
/* fasta indexing */
params.fasta = "$baseDir/data/bam/*.fasta"
params.annotation = "$baseDir/data/bam/*.gff3"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_file }
Channel
.fromPath( params.annotation )
.ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
.set { annotation_file }
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
file annotation from annotation_file
output:
file "*.index*" into index_files
script:
def cmd_annotation = "--gff3 ${annotation}"
if(annotation ==~ /.*\.gtf$/){
cmd_annotation = "--gtf ${annotation}"
}
"""
rsem-prepare-reference -p ${task.cpus} --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
${fasta.baseName}_rsem_bowtie2_report.txt
"""
}
/*
* for paired-end data
*/
params.fastq = "$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/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*" into counts_files
script:
index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
-output-genome-bam -p ${task.cpus} \
--paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
> ${pair_id}_rsem_bowtie2_report.txt
"""
}
/*
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 300
params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
log.info "mean read size: ${params.mean}"
log.info "sd read size: ${params.sd}"
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/quantification/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*" into count_files
script:
index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
${reads} ${index_name} ${tagname} > ${tagname}_rsem_bowtie2_report.txt
"""
}
params.fasta = "$baseDir/data/bam/*.fasta"
params.annotation = "$baseDir/data/bam/*.gff3"
log.info "fasta files : ${params.fasta}"
Channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.set { fasta_file }
Channel
.fromPath( params.annotation )
.ifEmpty { error "Cannot find any annotation files matching: ${params.annotation}" }
.set { annotation_file }
process index_fasta {
tag "$fasta.baseName"
cpus 4
publishDir "results/mapping/index/", mode: 'copy'
input:
file fasta from fasta_file
file annotation from annotation_file
output:
file "*.index*" into index_files
script:
def cmd_annotation = "--gff3 ${annotation}"
if(annotation ==~ /.*\.gtf$/){
cmd_annotation = "--gtf ${annotation}"
}
"""
rsem-prepare-reference -p ${task.cpus} --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
${cmd_annotation} ${fasta} ${fasta.baseName}.index > \
${fasta.baseName}_rsem_bowtie2_report.txt
"""
}
params.fastq = "$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/quantification/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
file index from index_files.toList()
output:
file "*" into counts_files
script:
index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
-output-genome-bam -p ${task.cpus} \
--paired-end ${reads[0]} ${reads[1]} ${index_name} ${pair_id} \
> ${pair_id}_rsem_bowtie2_report.txt
"""
}
params.fastq = "$baseDir/data/fastq/*.fastq"
params.index = "$baseDir/data/index/*.index*"
params.mean = 300
params.sd = 100
log.info "fastq files : ${params.fastq}"
log.info "index files : ${params.index}"
log.info "mean read size: ${params.mean}"
log.info "sd read size: ${params.sd}"
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/quantification/", mode: 'copy'
input:
file reads from fastq_files
file index from index_files.toList()
output:
file "*" into count_files
script:
index_name = (index[0].baseName =~ /(.*)\.\d/)[0][1]
"""
rsem-calculate-expression --bowtie2 \
--bowtie2-path \$(which bowtie2 | sed 's/bowtie2\$//g') \
--bowtie2-sensitivity-level "very_sensitive" \
--fragment-length-mean ${params.mean} --fragment-length-sd ${params.sd} \
--output-genome-bam -p ${task.cpus} \
${reads} ${index_name} ${reads.baseName} \
> ${reads.baseName}_rsem_bowtie2_report.txt
"""
}
nextflow src/nf_modules/RSEM/tests/index.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
--annotation "data/tiny_dataset/annot/tiny.gff"
nextflow src/nf_modules/RSEM/tests/quantification_single.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
nextflow src/nf_modules/RSEM/tests/quantification_paired.nf \
-c src/nf_modules/RSEM/rsem.config \
-profile docker \
--index "results/mapping/index/tiny_v2.index*" \
--fastq "data/tiny_dataset/fastq/tiny*_R{1,2}.fastq"