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Merge pull request #441 from ypriverol/dev
Improving configs for OpenMS dev and DIANN versions over 1.8.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| name: Fork-specific CI for test_latest_dia | ||
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| # Trigger only for your fork and the 'test_latest_dia' test profile | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| pull_request: | ||
| branches: | ||
| - dev | ||
| paths: | ||
| - "**.yml" | ||
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| env: | ||
| NXF_ANSI_LOG: false | ||
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| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
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| jobs: | ||
| test: | ||
| name: Run test_latest_dia with Docker | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| CAPSULE_LOG: none | ||
| TEST_PROFILE: test_latest_dia | ||
| EXEC_PROFILE: docker | ||
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| # Ensure this workflow only runs for your fork | ||
| if: ${{ github.repository == 'ypriverol/quantms' }} | ||
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| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
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| - name: Set up Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "24.04.2" # Or the Nextflow version you prefer | ||
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| - name: Log in to GitHub Container Registry | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| registry: ghcr.io | ||
| username: ${{ secrets.GHCR_USERNAME }} | ||
| password: ${{ secrets.GHCR_TOKEN }} | ||
|
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| - name: Run test_latest_dia with Docker | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results | ||
| - name: Gather failed logs | ||
| if: failure() || cancelled() | ||
| run: | | ||
| mkdir failed_logs | ||
| failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2) | ||
| while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed" | ||
| - uses: actions/upload-artifact@v4 | ||
| if: failure() || cancelled() | ||
| name: Upload failed logs | ||
| with: | ||
| name: failed_logs_${{ matrix.test_profile }}_${{ matrix.exec_profile }} | ||
| include-hidden-files: true | ||
| path: failed_logs | ||
| overwrite: false | ||
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| - uses: actions/upload-artifact@v4 | ||
| if: always() | ||
| name: Upload results | ||
| with: | ||
| name: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results | ||
| include-hidden-files: true | ||
| path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results | ||
| overwrite: false | ||
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| - uses: actions/upload-artifact@v4 | ||
| if: always() | ||
| name: Upload log | ||
| with: | ||
| name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}.log | ||
| include-hidden-files: true | ||
| path: .nextflow.log | ||
| overwrite: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for EMBL-EBI Codon Cluster for the SLURM login nodes | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Author: Yasset Perez-Riverol | ||
| Mail: [email protected] | ||
| URL: https://www.ebi.ac.uk/ | ||
| Basedon: https://github.com/nf-core/configs/blob/master/conf/ebi_codon_slurm.config | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
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| params { | ||
| config_profile_contact = "Yasset Perez-Riverol" | ||
| config_profile_description = "The European Bioinformatics Institute HPC cluster (codon) profile for the SLURM login nodes" | ||
| config_profile_url = "https://www.ebi.ac.uk/" | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| // the default is 20 minutes and fails with large images | ||
| pullTimeout = "3 hours" | ||
| autoMounts = false | ||
| runOptions = '-B /hps/nobackup/juan/pride/reanalysis:/hps/nobackup/juan/pride/reanalysis' | ||
| cacheDir = "/hps/nobackup/juan/pride/reanalysis/singularity/" | ||
| } | ||
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| process { | ||
| // this is to avoid errors for missing files due to shared filesystem latency | ||
| maxRetries = 30 | ||
| errorStrategy = { task.exitStatus == 0 ? "retry" : "terminate" } | ||
| cache = "lenient" | ||
| afterScript = "sleep 60" | ||
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| withName:PROTEOMICSLFQ{ | ||
| memory = {(mzmls as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt } | ||
| cpus = {(mzmls as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt } | ||
| } | ||
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| withName:ASSEMBLE_EMPIRICAL_LIBRARY{ | ||
| memory = {(ms_files as List).size() < 200 ? 72.GB * task.attempt : 250.GB * task.attempt} | ||
| cpus = {(ms_files as List).size() < 200 ? 12 * task.attempt : 24 * task.attempt } | ||
| } | ||
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| withLabel: diann { | ||
| container = '/hps/nobackup/juan/pride/reanalysis/singularity/ghcr.io-bigbio-diann-1.9.2.sif' | ||
| } | ||
| } | ||
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| executor { | ||
| name = "slurm" | ||
| queueSize = 2000 | ||
| submitRateLimit = "10/1sec" | ||
| exitReadTimeout = "30 min" | ||
| jobName = { | ||
| task.name | ||
| .replace("[", "(") | ||
| .replace("]", ")") | ||
| .replace(" ", "_") | ||
| } | ||
| } |
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