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atacseq_analysis
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BICF
Astrocyte
atacseq_analysis
Commits
48f97ee1
Commit
48f97ee1
authored
Jun 15, 2020
by
Venkat Malladi
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Fix track pipeline.
parent
ce0b51ce
Pipeline
#7193
canceled with stages
in 100 minutes and 3 seconds
Changes
2
Pipelines
1
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2 changed files
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7 additions
and
6 deletions
+7
-6
.gitlab-ci.yml
.gitlab-ci.yml
+2
-2
workflow/main.nf
workflow/main.nf
+5
-4
No files found.
.gitlab-ci.yml
View file @
48f97ee1
...
...
@@ -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
workflow/main.nf
View file @
48f97ee1
...
...
@@ -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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