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Merge pull request #91 from apeltzer/master

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Fix Github Actions tests
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Alexander Peltzer 2019-11-26 14:34:53 +01:00 committed by GitHub
commit 8ca2e808b4
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2 changed files with 16 additions and 11 deletions
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21
.github/workflows/main.yml vendored
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@ -1,9 +1,19 @@
name: Configs tests name: Configs tests
on: [pull_request, push]
jobs: 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: profile_test:
runs-on: ubuntu-latest runs-on: ubuntu-latest
name: Run individual profiles name: Run ${{ matrix.profile }} profile
needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', 'denbi_qbic', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh'] profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'czbiohub_aws_highpriority', 'czbiohub_aws', 'denbi_qbic', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
@ -13,8 +23,7 @@ jobs:
run: | run: |
wget -qO- get.nextflow.io | bash wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/ sudo mv nextflow /usr/local/bin/
- name: Check whether profiles are all tested - name: Check ${{ matrix.profile }} profile
run: | env:
python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml SCRATCH: '~'
- name: "Check profile" run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

6
conf/prince.config
View file

@ -18,10 +18,6 @@ singularity {
} }
process { process {
beforeScript = """ beforeScript = "module load $singularityModule $squashfsModule"
module load $singularityModule
module load $squashfsModule
"""
.stripIndent()
executor = 'slurm' executor = 'slurm'
} }