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BICF
Astrocyte
cellranger_mkfastq
Commits
458eec97
Commit
458eec97
authored
Dec 28, 2019
by
Gervaise Henry
🤠
Browse files
Set scripts as inputs
parent
028dbf32
Pipeline
#5387
passed with stages
in 5 minutes and 42 seconds
Changes
2
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
workflow/conf/biohpc_local.config
View file @
458eec97
...
...
@@ -2,23 +2,20 @@ process {
executor
=
'local'
container
=
'docker://bicf/bicfbase:1.3'
with
Label
:
checkDesignFile
{
container
=
'docker://bicf/python3:1.
2
'
with
Name
:
checkDesignFile
{
container
=
'docker://bicf/python3:1.
3
'
}
with
Label
:
untarBCL
{
with
Name
:
untarBCL
{
}
with
Label
:
mkfastq
{
with
Name
:
mkfastq
{
container
=
'docker://bicf/cellranger3.1.0:1.0'
}
with
Label
:
countDesign
{
with
Name
:
countDesign
{
}
with
Label
:
fastqc
{
module
= [
'fastqc/0.11.5'
,
'parallel'
]
with
Name
:
fastqc
{
container
=
'docker://bicf/fastqc:1.5'
}
withLabel
:
versions
{
module
= [
'python/3.6.1-2-anaconda'
,
'cellranger/3.0.2'
,
'bcl2fastq/2.19.1'
,
'fastqc/0.11.5'
]
}
withLabel
:
multiqc
{
withName
:
multiqc
{
container
=
'docker://bicf/multiqc:1.4'
}
}
...
...
workflow/main.nf
View file @
458eec97
...
...
@@ -8,7 +8,7 @@ main.nf
*
*/
// Define
I
nput variables
// Define
i
nput variables
params.name = "run"
params.bcl = "${baseDir}/../test_data/*.tar.gz"
params.designFile = "${baseDir}/../test_data/design.csv"
...
...
@@ -16,7 +16,7 @@ params.outDir = "${baseDir}/output"
params.multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
params.references = "${baseDir}/../docs/references.md"
// Define
L
ist of
F
iles
// Define
l
ist of
f
iles
tarList = Channel
.fromPath( params.bcl )
bclCount = Channel
...
...
@@ -32,12 +32,18 @@ outDir = params.outDir
multiqcConf = params.multiqcConf
references = params.references
// Define script files
check_designScript = Channel.fromPath("$baseDir/scripts/check_design.py")
untarBCLScript = Channel.fromPath("$baseDir/scripts/untarBCL.sh")
countDesignScript = Channel.fromPath("$baseDir/scripts/countDesign.sh")
fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
process checkDesignFile {
tag "${name}"
input:
file check_designScript
file designLocation
output:
...
...
@@ -52,7 +58,7 @@ process checkDesignFile {
if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
mv "${designLocation}" "\${noSpaceDesign}"
fi
python3
${baseDir}/scripts/
check_design.py -d \${noSpaceDesign}
python3 check_design.py -d \${noSpaceDesign}
"""
}
...
...
@@ -63,6 +69,7 @@ process untarBCL {
tag "${tar}"
input:
file untarBCLScript
file tar from tarList
output:
...
...
@@ -111,6 +118,7 @@ if (bclCount.value == 1) {
publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
input:
file countDesignScript
file fastqs from cellrangerCount.collect()
file design from designCount
...
...
@@ -119,7 +127,7 @@ if (bclCount.value == 1) {
script:
"""
bash
${baseDir}/scripts/
countDesign.sh
bash countDesign.sh
"""
}
...
...
@@ -132,6 +140,7 @@ process fastqc {
tag "${bclName}"
input:
file fastqcScript
file fastqPaths
val bclName
...
...
@@ -143,7 +152,7 @@ process fastqc {
hostname
ulimit -a
find *.fastq.gz -exec mv {} ${bclName}.{} \\;
bash
${baseDir}/scripts/
fastqc.sh
bash fastqc.sh
"""
}
...
...
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