mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Merge branch 'master' into master
This commit is contained in:
commit
5c39c1ed1a
2 changed files with 15 additions and 10 deletions
19
.github/workflows/main.yml
vendored
19
.github/workflows/main.yml
vendored
|
@ -1,9 +1,19 @@
|
|||
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
|
||||
profile_test:
|
||||
runs-on: ubuntu-latest
|
||||
name: Run individual profiles
|
||||
name: Run ${{ matrix.profile }} profile
|
||||
needs: test_all_profiles
|
||||
strategy:
|
||||
matrix:
|
||||
profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
|
||||
|
@ -13,8 +23,7 @@ jobs:
|
|||
run: |
|
||||
wget -qO- get.nextflow.io | bash
|
||||
sudo mv nextflow /usr/local/bin/
|
||||
- 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
|
||||
- name: "Check profile"
|
||||
- name: Check ${{ matrix.profile }} profile
|
||||
env:
|
||||
SCRATCH: '~'
|
||||
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
|
||||
|
|
|
@ -18,10 +18,6 @@ singularity {
|
|||
}
|
||||
|
||||
process {
|
||||
beforeScript = """
|
||||
module load $singularityModule
|
||||
module load $squashfsModule
|
||||
"""
|
||||
.stripIndent()
|
||||
beforeScript = "module load $singularityModule $squashfsModule"
|
||||
executor = 'slurm'
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue