Commit a34ccd98 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add in pipelinetracking.

parent ea6b9d45
Pipeline #7300 passed with stages
in 1042 minutes and 26 seconds
...@@ -39,7 +39,7 @@ single_end_mouse: ...@@ -39,7 +39,7 @@ single_end_mouse:
only: only:
- master - master
script: 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 - pytest -m singleend
paired_end_human: paired_end_human:
...@@ -49,7 +49,7 @@ paired_end_human: ...@@ -49,7 +49,7 @@ paired_end_human:
except: except:
- master - master
script: 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 - pytest -m pairedend
single_end_single_control: single_end_single_control:
...@@ -59,7 +59,7 @@ single_end_single_control: ...@@ -59,7 +59,7 @@ single_end_single_control:
except: except:
- master - master
script: 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 - pytest -m singlecontrol
single_end_diff: single_end_diff:
...@@ -67,7 +67,7 @@ single_end_diff: ...@@ -67,7 +67,7 @@ single_end_diff:
only: only:
- master - master
script: 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 singleend
- pytest -m singlediff - pytest -m singlediff
...@@ -78,7 +78,7 @@ paired_end_diff: ...@@ -78,7 +78,7 @@ paired_end_diff:
- master - master
stage: multiple stage: multiple
script: 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 pairedend
- pytest -m paireddiff - pytest -m paireddiff
artifacts: artifacts:
...@@ -93,7 +93,7 @@ single_end_skip: ...@@ -93,7 +93,7 @@ single_end_skip:
only: only:
- master - master
script: 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 - pytest -m singleskip_true
cleanup_job: cleanup_job:
......
...@@ -28,6 +28,9 @@ params.skipMotif = false ...@@ -28,6 +28,9 @@ params.skipMotif = false
params.skipPlotProfile = false params.skipPlotProfile = false
params.references = "$baseDir/../docs/references.md" params.references = "$baseDir/../docs/references.md"
params.multiqc = "$baseDir/conf/multiqc_config.yaml" params.multiqc = "$baseDir/conf/multiqc_config.yaml"
params.ci = false
params.dev = false
// Assign variables if astrocyte // Assign variables if astrocyte
if (params.astrocyte) { if (params.astrocyte) {
...@@ -101,6 +104,31 @@ multiqc = params.multiqc ...@@ -101,6 +104,31 @@ multiqc = params.multiqc
gtfFile = params.gtf gtfFile = params.gtf
geneNames = params.geneNames 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 // Check design file for errors
process checkDesignFile { 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