mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 09:09:56 +00:00
99 lines
2.5 KiB
YAML
99 lines
2.5 KiB
YAML
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"
|
||
- "alice"
|
||
- "aws_tower"
|
||
- "awsbatch"
|
||
- "azurebatch"
|
||
- "bi"
|
||
- "bigpurple"
|
||
- "binac"
|
||
- "biohpc_gen"
|
||
- "cambridge"
|
||
- "leicester"
|
||
- "cbe"
|
||
- "ccga_dx"
|
||
- "ccga_med"
|
||
- "cedars"
|
||
- "cfc"
|
||
- "cfc_dev"
|
||
- "cheaha"
|
||
- "computerome"
|
||
- "crick"
|
||
- "denbi_qbic"
|
||
- "ebc"
|
||
- "eddie"
|
||
- "eva"
|
||
- "fgcz"
|
||
- "genotoul"
|
||
- "genouest"
|
||
- "gis"
|
||
- "google"
|
||
- "hasta"
|
||
- "hebbe"
|
||
- "icr_davros"
|
||
- "ifb_core"
|
||
- "imperial"
|
||
- "jax"
|
||
- "lugh"
|
||
- "marvin"
|
||
- "maestro"
|
||
- "mpcdf"
|
||
- "munin"
|
||
- "nu_genomics"
|
||
- "nihbiowulf"
|
||
- "oist"
|
||
- "pasteur"
|
||
- "phoenix"
|
||
- "prince"
|
||
- "rosalind"
|
||
- "sahmri"
|
||
- "sanger"
|
||
- "seg_globe"
|
||
- "uct_hpc"
|
||
- "unibe_ibu"
|
||
- "uppmax"
|
||
- "utd_ganymede"
|
||
- "utd_sysbio"
|
||
- "uzh"
|
||
- "vai"
|
||
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 }} profile
|
||
env:
|
||
SCRATCH: "~"
|
||
NXF_GLOBAL_CONFIG: awsbatch.config
|
||
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf -profile ${{ matrix.profile }}
|