Commit 76777f0c authored by Venkat Malladi's avatar Venkat Malladi

Resolve merge on testing params.

parents fad31e6d df7ed9bf
Pipeline #6582 passed with stages
in 998 minutes and 39 seconds
variables:
GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_CONCURRENT_ID/$CI_PROJECT_PATH/$CI_JOB_STAGE/$CI_JOB_NAME
before_script:
- module add python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load nextflow/0.31.0
- ulimit -Ss unlimited
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
stages:
......@@ -14,6 +10,7 @@ stages:
- single
- multiple
- skip
- cleanup
user_configuration:
stage: unit
......@@ -27,13 +24,15 @@ astrocyte:
- module unload nextflow
- cd ..
- astrocyte_cli validate chipseq_analysis
after_script:
- rm -rf work/
single_end_mouse:
stage: single
only:
- master
script:
- nextflow run workflow/main.nf --astrocyte true
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true
- pytest -m singleend
paired_end_human:
......@@ -43,7 +42,7 @@ paired_end_human:
except:
- master
script:
- nextflow run workflow/main.nf --designFile "$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 "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- pytest -m pairedend
single_end_single_control:
......@@ -53,7 +52,7 @@ single_end_single_control:
except:
- master
script:
- nextflow run workflow/main.nf --designFile "$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 "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
- pytest -m singlecontrol
single_end_diff:
......@@ -61,7 +60,7 @@ single_end_diff:
only:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
- pytest -m singleend
- pytest -m singlediff
......@@ -72,7 +71,7 @@ paired_end_diff:
- master
stage: multiple
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
- pytest -m pairedend
- pytest -m paireddiff
......@@ -81,5 +80,12 @@ single_end_skip:
only:
- master
script:
- nextflow run workflow/main.nf --designFile "$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
- pytest -m singleskip_true
cleanup_job:
stage: cleanup
script:
- cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
- rm -fr $CI_PIPELINE_ID/
......@@ -4,8 +4,10 @@
# BICF ChIP-seq Pipeline
[![Build Status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/build.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![Coverage Report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/commits/master)
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.24.0-brightgreen.svg
)](https://www.nextflow.io/)
[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.2.0-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
......
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