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name : Configs tests
on : [ pull_request, push]
jobs :
test_all_profiles :
runs-on : ubuntu-latest
name : Check if all profiles are tested
steps :
- uses : actions/checkout@v1
- 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@v1
- 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"
- "aws_tower"
- "awsbatch"
- "azurebatch"
- "bi"
- "bigpurple"
- "binac"
- "biohpc_gen"
- "cambridge"
- "leicester"
- "cbe"
- "ccga_dx"
- "ccga_med"
- "cedars"
- "cfc"
- "cfc_dev"
- "cheaha"
- "computerome"
- "crg"
- "crick"
- "crukmi"
- "denbi_qbic"
- "ebc"
- "eddie"
- "eva"
- "fgcz"
- "genotoul"
- "genouest"
- "gis"
- "google"
- "hasta"
- "hebbe"
- "hki"
- "icr_davros"
- "ifb_core"
- "imperial"
- "jax"
- "ku_sund_dangpu"
- "lugh"
- "mana"
- "marvin"
- "medair"
- "mjolnir_globe"
- "maestro"
- "mpcdf"
- "munin"
- "nu_genomics"
- "nihbiowulf"
- "oist"
- "pasteur"
- "phoenix"
- "prince"
- "rosalind"
- "sage"
- "sahmri"
- "sanger"
- "sbc_sharc"
- "seg_globe"
- "tigem"
- "ucl_myriad"
- "uct_hpc"
- "unibe_ibu"
- "uppmax"
- "utd_ganymede"
- "utd_sysbio"
- "uzh"
- "vai"
- "vsc_ugent"
steps :
- uses : actions/checkout@v1
- name : Install Nextflow
run : |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name : Check ${{ matrix.profile }}
env :
SCRATCH : "~"
NXF_GLOBAL_CONFIG : awsbatch.config
run : nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }}