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lanani
nextflow
Commits
1041a4af
Verified
Commit
1041a4af
authored
Jul 03, 2018
by
Laurent Modolo
Browse files
Merge branch 'cigogne/nextflow-master' into dev
parents
686a58f8
52b510e4
Changes
5
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src/nf_modules/sra-tools/sra-tools.config
0 → 100644
View file @
1041a4af
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"
}
}
}
}
src/nf_modules/sra-tools/sra-tools.nf
0 → 100644
View file @
1041a4af
/*
* 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 ${x.run}.fastq
fi
"""
}
src/nf_modules/sra-tools/tests/fastqdump.nf
0 → 100644
View file @
1041a4af
/*
* sra-tools :
*/
/* fastq-dump
* Imputs : srr list
* Outputs : fastq files
*/
params.list_srr = "$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
"""
}
src/nf_modules/sra-tools/tests/list-srr.txt
0 → 100644
View file @
1041a4af
run
ERR572281
ERR572146
ERR572201
ERR638114
ERR638115
ERR638116
src/nf_modules/sra-tools/tests/tests.sh
0 → 100755
View file @
1041a4af
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"
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