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lanani
nextflow
Commits
8f2c8522
Verified
Commit
8f2c8522
authored
Jul 25, 2018
by
Laurent Modolo
Browse files
Merge branch 'elabaron/nextflow-master' into dev to get FastQC modif
from
@elabaron
parents
4be336cf
49faa7f0
Changes
3
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src/docker_modules/FastQC/0.11.5/Dockerfile
View file @
8f2c8522
...
...
@@ -2,7 +2,8 @@ FROM ubuntu:18.04
MAINTAINER
Laurent Modolo
ENV
FASTQC_VERSION=0.11.5
ENV
PACKAGES fastqc=${FASTQC_VERSION}*
ENV
PACKAGES fastqc=${FASTQC_VERSION}* \
perl
RUN
apt-get update
&&
\
apt-get
install
-y
--no-install-recommends
${
PACKAGES
}
&&
\
...
...
src/nf_modules/FastQC/fastqc.config
0 → 100644
View file @
8f2c8522
profiles
{
docker
{
docker
.
temp
=
'auto'
docker
.
enabled
=
true
process
{
$
fastqc
{
container
=
"fastqc:0.11.5"
}
}
}
sge
{
process
{
$
fastqc
{
beforeScript
=
"module purge; module load FastQC/0.11.5"
executor
=
"sge"
cpus
=
1
memory
=
"5GB"
time
=
"6h"
queueSize
=
1000
pollInterval
=
'60sec'
queue
=
'monointeldeb128'
}
}
}
}
src/nf_modules/FastQC/fastqc.nf
0 → 100644
View file @
8f2c8522
/*
* fastqc :
* Imputs : fastq files
* Output : pdf files
*/
/* fastQC */
params.fastq = ""
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process fastqc {
tag "$fastq.baseName"
publishDir "results/fastqc/", mode: 'copy'
input:
file fastq from fastq_files
output:
file "*.htlm" into fastqc_repport
script:
"""
fastqc -o ./ --noextract -f fastq ${fastq}
"""
}
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