Merge pull request #689 from RoganGrant/master #2449
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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 }} |