Merge branch 'ci-merge-test' into 'master'

Ci merge test

Closes #79 and #80

See merge request !68

.gitlab-ci.yml

@@ -2,7 +2,6 @@ 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 -c unlimited
   - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
 
 stages:
@@ -11,6 +10,7 @@ stages:
   - single
   - multiple
   - skip
+  - cleanup
 
 user_configuration:
   stage: unit
@@ -24,13 +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:
@@ -40,7 +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:
@@ -50,7 +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:
@@ -60,7 +62,7 @@ single_end_diff:
   except:
     - 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
 
@@ -69,7 +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
 
@@ -78,5 +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/

README.md

@@ -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)