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