Commit ad917147 authored by Venkat Malladi's avatar Venkat Malladi

Merge branch '80-concurrent_issue' into ci-merge-test

parents d7f31c15 fa258f22
Pipeline #6413 failed with stages
in 247 minutes and 56 seconds
variables:
GIT_DEPTH: 5
GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_CONCURRENT_ID/$CI_PROJECT_NAME/$CI_PIPELINE_ID
GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME/$CI_PIPELINE_ID/$CI_CONCURRENT_ID/$CI_JOB_ID/
before_script:
......@@ -16,6 +16,7 @@ stages:
- single
- multiple
- skip
- cleanup
user_configuration:
stage: unit
......@@ -29,6 +30,8 @@ astrocyte:
- module unload nextflow
- cd ..
- astrocyte_cli validate chipseq_analysis
after_script:
- rm -rf work/
single_end_mouse:
stage: single
......@@ -37,6 +40,8 @@ single_end_mouse:
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true
- pytest -m singleend
after_script:
- rm -rf work/
paired_end_human:
stage: single
......@@ -47,6 +52,8 @@ paired_end_human:
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- pytest -m pairedend
after_script:
- rm -rf work/
single_end_single_control:
stage: single
......@@ -57,6 +64,8 @@ single_end_single_control:
script:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
- pytest -m singlecontrol
after_script:
- rm -rf work/
single_end_diff:
stage: multiple
......@@ -68,6 +77,8 @@ single_end_diff:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
- pytest -m singleend
- pytest -m singlediff
after_script:
- rm -rf work/
paired_end_diff:
only:
......@@ -77,6 +88,8 @@ paired_end_diff:
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- pytest -m pairedend
- pytest -m paireddiff
after_script:
- rm -rf work/
single_end_skip:
stage: skip
......@@ -85,3 +98,12 @@ single_end_skip:
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
- pytest -m singleskip_true
after_script:
- rm -rf work/
cleanup_job:
stage: cleanup
script:
- cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
- rm -fr $CI_PIPELINE_ID/
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