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Update biohpc_gen.config for future nextflow #2612

Update biohpc_gen.config for future nextflow

Update biohpc_gen.config for future nextflow #2612

Workflow file for this run

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"
- "bih"
- "binac"
- "biohpc_gen"
- "biowulf"
- "bluebear"
- "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"
- "embl_hd"
- "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_danhead"
- "leicester"
- "lugh"
- "m3c"
- "maestro"
- "mana"
- "marjorie"
- "marvin"
- "mccleary"
- "medair"
- "mjolnir_globe"
- "mpcdf"
- "mpcdf_viper"
- "munin"
- "nci_gadi"
- "nu_genomics"
- "nygc"
- "nyu_hpc"
- "oist"
- "pasteur"
- "pawsey_nimbus"
- "pawsey_setonix"
- "pdc_kth"
- "phoenix"
- "psmn"
- "qmul_apocrita"
- "rosalind"
- "rosalind_uge"
- "roslin"
- "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_ganymede"
- "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 }}