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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
Commits
bb5133f0
Commit
bb5133f0
authored
Jun 21, 2020
by
Venkat Malladi
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Merge branch '84-tracking' into 'dev'
Add in pipelinetracking. See merge request
!70
parents
ea6b9d45
a34ccd98
Pipeline
#7372
passed with stages
in 1162 minutes
Changes
2
Pipelines
1
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2 changed files
with
34 additions
and
6 deletions
+34
-6
.gitlab-ci.yml
.gitlab-ci.yml
+6
-6
workflow/main.nf
workflow/main.nf
+28
-0
No files found.
.gitlab-ci.yml
View file @
bb5133f0
...
...
@@ -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
:
...
...
workflow/main.nf
View file @
bb5133f0
...
...
@@ -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 {
...
...
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