fix path to hg38 combined blacklist #39
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| paths-ignore: | |
| - '*.md' | |
| - '*.ignore' | |
| - LICENSE | |
| - Dockerfile # as we build and push manually right now | |
| - environment.yml # as we build and push manually right now | |
| jobs: | |
| atac_chip_preprocess_ci: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: INSTALL-NEXTFLOW | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: TEST-DOCKER-ATACseq | |
| run: | | |
| NXF_VER=23.04.0 nextflow run main.nf -profile test,docker --keep_merge --keep_trim | |
| - name: Commit software versions | |
| run: | | |
| git config --global user.name 'atpoint' | |
| git config --global user.email '[email protected]' | |
| mkdir -p misc && cp atac_chip_preprocess_results/pipeline_info/*.txt misc/ | |
| git add misc/*.txt | |
| if (( $(git status -s | grep -c 'misc/') > 0 )); then | |
| git commit -am "update software version and command line reports" | |
| git push -f | |
| fi | |
| - name: TEST-DOCKER-ChIPseq | |
| run: | | |
| NXF_VER=23.04.0 nextflow run main.nf -profile test,docker --keep_merge --keep_trim --atacseq false --macs_additional '\--keep-dup=all --nomodel --extsize 150' |