Commit 56e90538 authored by Venkat Malladi's avatar Venkat Malladi

Fix pipeline.

parent 48f97ee1
Pipeline #7201 failed with stages
in 3 minutes and 4 seconds
......@@ -30,7 +30,7 @@ single_end_human:
- branches
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci true
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci true --dev true
- pytest -m singleend_human
......@@ -40,5 +40,5 @@ paired_end_mouse:
- branches
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true --ci true
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true --ci true --dev true
- pytest -m pairedend_mouse
......@@ -21,6 +21,7 @@ params.outDir= "${baseDir}/output"
params.references = "${baseDir}/../docs/references.md"
params.multiqc = "${baseDir}/conf/multiqc_config.yaml"
params.ci = false
params.dev = false
// Check inputs
if(params.bwaIndex) {
......@@ -71,7 +72,8 @@ process trackStart {
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", \
"pipelineVersion": "2.0.0", \
"ci": ${params.ci}}' \
"ci": '${params.ci}}' \
"dev": '${params.dev}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
......
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