Verified Commit 1041a4af authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Merge branch 'cigogne/nextflow-master' into dev

parents 686a58f8 52b510e4
profiles {
docker {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqdump {
container = "sratoolkit:2.8.2"
} }
}
sge {
process{
$fastqdump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2"
}
}
}
}
/*
* sra-tools :
*/
/* fastq-dump
* Imputs : srr list
* Outputs : fastq files
*/
params.list_srr = "$baseDir/data/SRR/*.txt"
log.info "downloading list srr : ${params.list_srr}"
Channel
.fromPath( params.list_srr )
.ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
.splitCsv(header: true)
.set { SRR }
//run is the column name containing SRR ids
process fastq-dump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
input:
val x from SRR
output:
file("*") into fastq
script:
"""
fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" ${x.run}
if [ -f ${x.run}_1.fastq ]
then
true
else
touch ${x.run}.fastq
fi
"""
}
/*
* sra-tools :
*/
/* fastq-dump
* Imputs : srr list
* Outputs : fastq files
*/
params.list_srr = "$baseDir/data/SRR/*.txt"
log.info "downloading list srr : ${params.list_srr}"
Channel
.fromPath( params.list_srr )
.ifEmpty { error "Cannot find any bam files matching: ${params.list_srr}" }
.splitCsv(header: true)
.set { SRR }
//run is the column name containing SRR ids
process fastqdump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
input:
val x from SRR
output:
file("*") into fastq
script:
"""
#for test only 10000 reads are downloading with the option -N 10000 -X 20000
fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" -N 10000 -X 20000 ${x.run}
if [ -f ${x.run}_1.fastq ]
then
true
else
touch ${x.run}.fastq
fi
"""
}
run
ERR572281
ERR572146
ERR572201
ERR638114
ERR638115
ERR638116
nextflow src/nf_modules/sra-tools/tests/fastqdump.nf \
-c src/nf_modules/sra-tools/sra-tools.config \
-profile docker \
--list_srr "src/nf_modules/sra-tools/tests/list-srr.txt"
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment