Commit 48f97ee1 authored by Venkat Malladi's avatar Venkat Malladi

Fix track pipeline.

parent ce0b51ce
Pipeline #7193 canceled with stages
in 100 minutes and 3 seconds
......@@ -30,7 +30,7 @@ single_end_human:
- branches
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci 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 "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd true --blacklist true --astrocyte true --ci true
- pytest -m pairedend_mouse
......@@ -20,6 +20,7 @@ params.astrocyte = false
params.outDir= "${baseDir}/output"
params.references = "${baseDir}/../docs/references.md"
params.multiqc = "${baseDir}/conf/multiqc_config.yaml"
params.ci = false
// Check inputs
if(params.bwaIndex) {
......@@ -54,7 +55,7 @@ geneNames = params.geneNames
/*
* trackStart: track start of pipeline
*/
params.ci = false
process trackStart {
script:
"""
......@@ -64,12 +65,12 @@ process trackStart {
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "${workflow.manifest.name}", \
"pipeline": "atacseq_analysis", \
"start": "${workflow.start}", \
"astrocyte": ${params.astrocyte}, \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}",
"pipelineVersion": "${workflow.manifest.version}",
"nextflowVersion": "${workflow.nextflow.version}", \
"pipelineVersion": "2.0.0", \
"ci": ${params.ci}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
......
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