Commit bb5133f0 authored by Venkat Malladi's avatar Venkat Malladi

Merge branch '84-tracking' into 'dev'

Add in pipelinetracking.

See merge request !70
parents ea6b9d45 a34ccd98
Pipeline #7372 passed with stages
in 1162 minutes
......@@ -39,7 +39,7 @@ single_end_mouse:
only:
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true --ci true --dev true
- pytest -m singleend
paired_end_human:
......@@ -49,7 +49,7 @@ paired_end_human:
except:
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false --ci true --dev true
- pytest -m pairedend
single_end_single_control:
......@@ -59,7 +59,7 @@ single_end_single_control:
except:
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false --ci true --dev true
- pytest -m singlecontrol
single_end_diff:
......@@ -67,7 +67,7 @@ single_end_diff:
only:
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false --ci true --dev true
- pytest -m singleend
- pytest -m singlediff
......@@ -78,7 +78,7 @@ paired_end_diff:
- master
stage: multiple
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf --ci true --dev true
- pytest -m pairedend
- pytest -m paireddiff
artifacts:
......@@ -93,7 +93,7 @@ single_end_skip:
only:
- master
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false --ci true --dev true
- pytest -m singleskip_true
cleanup_job:
......
......@@ -28,6 +28,9 @@ params.skipMotif = false
params.skipPlotProfile = false
params.references = "$baseDir/../docs/references.md"
params.multiqc = "$baseDir/conf/multiqc_config.yaml"
params.ci = false
params.dev = false
// Assign variables if astrocyte
if (params.astrocyte) {
......@@ -101,6 +104,31 @@ multiqc = params.multiqc
gtfFile = params.gtf
geneNames = params.geneNames
/*
* trackStart: track start of pipeline
*/
process trackStart {
script:
"""
hostname
ulimit -a
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "chipseq_analysis", \
"start": "${workflow.start}", \
"astrocyte": ${params.astrocyte}, \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", \
"pipelineVersion": "1.1.1", \
"ci": ${params.ci}, \
"dev": ${params.dev}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
// Check design file for errors
process checkDesignFile {
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment