fix: $SLURM_JOBID is now $SLURM_JOB_ID on biowulf #2441
Workflow file for this run
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| name: Configs tests | |
| on: [pull_request, push] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test_all_profiles: | |
| runs-on: ubuntu-latest | |
| name: Check if all profiles are tested | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check whether profiles are all tested | |
| run: python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml | |
| check_nextflow_config: | |
| runs-on: ubuntu-latest | |
| name: Check if nextflow config runs in repository root | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - run: nextflow config -show-profiles ${GITHUB_WORKSPACE} | |
| profile_test: | |
| runs-on: ubuntu-latest | |
| name: Run ${{ matrix.profile }} profile | |
| needs: test_all_profiles | |
| strategy: | |
| matrix: | |
| profile: | |
| - "abims" | |
| - "adcra" | |
| - "alice" | |
| - "apollo" | |
| - "arcc" | |
| - "aws_tower" | |
| - "awsbatch" | |
| - "azurebatch" | |
| - "bi" | |
| - "bigpurple" | |
| - "binac" | |
| - "biohpc_gen" | |
| - "biowulf" | |
| - "cambridge" | |
| - "cbe" | |
| - "ccga_dx" | |
| - "ccga_med" | |
| - "cedars" | |
| - "ceres" | |
| - "cfc" | |
| - "cfc_dev" | |
| - "cheaha" | |
| - "computerome" | |
| - "create" | |
| - "crg" | |
| - "crick" | |
| - "crukmi" | |
| - "csiro_petrichor" | |
| - "daisybio" | |
| - "denbi_qbic" | |
| - "dkfz" | |
| - "ebc" | |
| - "ebi_codon" | |
| - "ebi_codon_slurm" | |
| - "eddie" | |
| - "engaging" | |
| - "einstein" | |
| - "ethz_euler" | |
| - "eva" | |
| - "fgcz" | |
| - "fub_curta" | |
| - "genotoul" | |
| - "genouest" | |
| - "gis" | |
| - "google" | |
| - "googlebatch" | |
| - "googlels" | |
| - "hasta" | |
| - "hki" | |
| - "hypatia" | |
| - "icr_davros" | |
| - "ifb_core" | |
| - "imb" | |
| - "ilifu" | |
| - "imperial" | |
| - "incliva" | |
| - "ipop_up" | |
| - "janelia" | |
| - "jax" | |
| - "jex" | |
| - "ku_sund_dangpu" | |
| - "leicester" | |
| - "lugh" | |
| - "m3c" | |
| - "maestro" | |
| - "mana" | |
| - "marjorie" | |
| - "marvin" | |
| - "mccleary" | |
| - "medair" | |
| - "mjolnir_globe" | |
| - "mpcdf" | |
| - "munin" | |
| - "nci_gadi" | |
| - "nu_genomics" | |
| - "nygc" | |
| - "nyu_hpc" | |
| - "oist" | |
| - "pasteur" | |
| - "pawsey_nimbus" | |
| - "pawsey_setonix" | |
| - "pdc_kth" | |
| - "phoenix" | |
| - "psmn" | |
| - "qmul_apocrita" | |
| - "rosalind" | |
| - "rosalind_uge" | |
| - "sage" | |
| - "sahmri" | |
| - "sanger" | |
| - "scw" | |
| - "seawulf" | |
| - "self_hosted_runner" | |
| - "seg_globe" | |
| - "software_license" | |
| - "tigem" | |
| - "tubingen_apg" | |
| - "tufts" | |
| - "tuos_stanage" | |
| - "ucl_cscluster" | |
| - "ucl_myriad" | |
| - "uct_hpc" | |
| - "ucd_sonic" | |
| - "uge" | |
| - "unibe_ibu" | |
| - "unc_lccc" | |
| - "unc_longleaf" | |
| - "uod_hpc" | |
| - "uppmax" | |
| - "utd_europa" | |
| - "utd_ganymede" | |
| - "utd_sysbio" | |
| - "uw_hyak_pedslabs" | |
| - "uzh" | |
| - "uzl_omics" | |
| - "vai" | |
| - "vsc_calcua" | |
| - "vsc_kul_uhasselt" | |
| - "vsc_ugent" | |
| - "wehi" | |
| - "wustl_htcf" | |
| - "xanadu" | |
| - "york_viking" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "latest-everything" | |
| - name: Check ${{ matrix.profile }} profile | |
| env: | |
| SCRATCH: "~" | |
| NXF_GLOBAL_CONFIG: awsbatch.config | |
| run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }} |