Commit 8f3b2fe6 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Updates, CI, config, main, check_design

parent f8e6940f
Pipeline #3343 failed with stages
before_script:
- module load python/3.6.1-2-anaconda
- module load nextflow/0.27.6
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_mkfastq/*tar.gz test_data/
- module load nextflow/0.31.1_Ignite
- mkdir test_data/simple
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/* test_data/simple/
stages:
- integration
- astrocyte
- simple
astrocyte_check:
stage: astrocyte
script:
- astrocyte_cli check ../cellranger_mkfastq
simple_test:
stage: integration
stage: simple
script:
- nextflow run workflow/main.nf
- nextflow run workflow/main.nf --bcl test_data/simple/*.tar.gz --designFile test_data/simple/cellranger-tiny-bcl-simple-1_2_0.csv
......@@ -8,6 +8,7 @@ process {
executor = 'local'
}
$untarBCL {
module = ['pigz/2.4']
queue = 'super'
}
$mkfastq {
......
......@@ -6,14 +6,16 @@
// Define Input variables
params.bcl = "$baseDir/../test_data/*.tar.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.outDir = "$baseDir/output"
// Define List of Files
tarList = Channel.fromPath( params.bcl )
// Define regular variables
designLocation = Channel
.fromPath(params.designFile)
.ifEmpty { exit 1, "design file not found: ${params.designFile}" }
outDir = params.outDir
process checkDesignFile {
......@@ -21,11 +23,11 @@ process checkDesignFile {
input:
params.designFile
file designLocation
output:
file("design.csv") into designPaths
file("design.checked.csv") into designPaths
script:
......@@ -33,7 +35,7 @@ process checkDesignFile {
hostname
ulimit -a
module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/check_design.py -d $params.designFile
python3 $baseDir/scripts/check_design.py -d $designLocation
"""
}
......@@ -65,7 +67,7 @@ process untarBCL {
process mkfastq {
tag "${bcl.baseName}"
publishDir "$outDir/${task.process}/${bcl.baseName}", mode: 'copy'
publishDir "$outDir/${task.process}", mode: 'copy'
input:
......
......@@ -70,7 +70,7 @@ def main():
# Check design file
new_design_df = check_design_headers(design_df)
new_design_df.to_csv('design.csv', header=True, sep=',', index=False)
new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
if __name__ == '__main__':
main()
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