Substantial rewrite of the pipeline #152
Workflow file for this run
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| # Copyright (C) 2022 Roberto Rossini (roberros@uio.no) | |
| # SPDX-License-Identifier: MIT | |
| name: CI | |
| on: | |
| push: | |
| branches: [ main, devel ] | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - ".dockerignore" | |
| - "env.yml" | |
| - "main.nf" | |
| - "nextflow.config" | |
| - "bin/*.py" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - ".dockerignore" | |
| - "env.yml" | |
| - "main.nf" | |
| - "nextflow.config" | |
| - "bin/*.py" | |
| release: | |
| types: [ published ] | |
| # https://stackoverflow.com/a/72408109 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| TEST_DATASET_URL: 'https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8b9d6836-0d6b-4c2f-9eaa-323f4fd7b6e4/4DNFI74YHN5W.mcool' | |
| TEST_DATASET_SHA256: 'a5e3dc9e9e6b68b577c086dcbf34e8a21094bf34fa27461440642e9273ee228b' | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| preproc-test-dataset: | |
| name: Preprocess test dataset | |
| runs-on: ubuntu-latest | |
| outputs: | |
| cache-key: ${{ steps.generate-cache-key.outputs.key }} | |
| steps: | |
| - name: Generate cache key | |
| id: generate-cache-key | |
| run: | | |
| key="test-dataset-$TEST_DATASET_SHA256" | |
| echo "key=$key" >> $GITHUB_OUTPUT | |
| - name: Cache test datasets | |
| id: cache-dataset | |
| uses: actions/cache@v3 | |
| with: | |
| key: ${{ steps.generate-cache-key.outputs.key }} | |
| path: data/ | |
| - name: Download test dataset | |
| if: steps.cache-dataset.outputs.cache-hit != 'true' | |
| run: | | |
| mkdir data | |
| cd data | |
| curl -LO "$TEST_DATASET_URL" | |
| - name: Checksum test dataset | |
| if: steps.cache-dataset.outputs.cache-hit != 'true' | |
| run: | | |
| echo "$TEST_DATASET_SHA256 data/$(basename "$TEST_DATASET_URL")" > checksum.sha256 | |
| shasum -c checksum.sha256 | |
| - name: Generate requirements.txt | |
| if: steps.cache-dataset.outputs.cache-hit != 'true' | |
| run: | | |
| echo 'cooler==0.10.0' > requirements.txt | |
| - name: Setup Python | |
| if: steps.cache-dataset.outputs.cache-hit != 'true' | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| cache: pip | |
| - name: Remove unused resolutions | |
| if: steps.cache-dataset.outputs.cache-hit != 'true' | |
| run: | | |
| src="data/$(basename "$TEST_DATASET_URL")" | |
| dest="$src.new" | |
| pip3 install -r requirements.txt | |
| cooler cp "$src::/resolutions/100000" "$dest" | |
| mv "$dest" "$src" | |
| test-workflow: | |
| name: Test workflow | |
| runs-on: ubuntu-latest | |
| needs: [ preproc-test-dataset ] | |
| strategy: | |
| matrix: | |
| NXF_VER: [ "22.10.8", "latest-stable" ] | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Cache test datasets | |
| uses: actions/cache@v3 | |
| with: | |
| key: ${{ needs.preproc-test-dataset.outputs.cache-key }} | |
| path: data/ | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: ${{ matrix.NXF_VER }} | |
| - name: Test workflow | |
| run: | | |
| nextflow run -c config/test.config \ | |
| --sample="test" \ | |
| --hic_file="data/$(basename "$TEST_DATASET_URL")" \ | |
| --resolution=100000 \ | |
| --outdir=data/out \ | |
| --max_cpus=$(nproc) \ | |
| --max_memory=6.GB \ | |
| --max_time=2.h \ | |
| . | |
| ls -lah data/out/cliques/test_{all,cis,trans}_{cliques,domains}*.gz |