Verified Commit b74bc642 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

Cleanup SRAtoolkit files

parent a2cdaddc
......@@ -89,7 +89,7 @@ Kallisto | ok | ok | ok
MultiQC | ok | ok | ok
RSEM | ok | ok | ok
SAMtools | ok | ok | ok
SRAtoolkit | **no** | ok | ok
SRAtoolkit | ok | ok | ok
Salmon | **no** | ok | ok
TopHat | **no** | ok | ok
Trimmomatic | **no** | ok | ok
......@@ -99,8 +99,6 @@ cutadapt | ok | ok | ok
deepTools | **no** | ok | ok
file_handle | **no** | ok | ok
pigz | **no** | ok | ok
sra-tools | ok | **no** | **no**
## Contributing
......
......@@ -3,14 +3,22 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
$fastqdump {
container = "sratoolkit:2.8.2"
} }
$fastq_dump {
container = "sratoolkit:2.8.2"
}
}
}
sge {
process{
$fastqdump {
$fastq_dump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2"
executor = "sge"
cpus = 1
memory = "5GB"
time = "6h"
queueSize = 1000
pollInterval = '60sec'
queue = 'monointeldeb128'
}
}
}
......
......@@ -20,24 +20,24 @@ Channel
//run is the column name containing SRR ids
process fastq-dump {
process fastq_dump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
input:
val x from SRR
val x from SRR
output:
file("*") into fastq
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
"""
}
fastq-dump --split-files --defline-seq '@\$ac_\$si/\$ri' --defline-qual "+" ${x.run}
if [ -f ${x.run}_1.fastq ]
then
true
else
touch ${x.run}.fastq
fi
"""
}
......@@ -20,24 +20,25 @@ Channel
//run is the column name containing SRR ids
process fastqdump {
process fastq_dump {
tag {"${x.run}"}
publishDir "results/download/fastq/${x.run}/", mode: 'copy'
input:
val x from SRR
val x from SRR
output:
file("*") into fastq
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
"""
}
#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
"""
}
nextflow src/nf_modules/SRAtoolkit/tests/fastqdump.nf \
-c src/nf_modules/SRAtoolkit/sratoolkit.config \
-profile docker \
--list_srr "src/nf_modules/SRAtoolkit/tests/list-srr.txt"
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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