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declate NXF_GLOBAL_CONFIG in ci

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This commit is contained in:
Piotr Faba 2020-05-27 16:30:00 +02:00
parent 2685275952
commit 66f191a1cf
2 changed files with 7 additions and 5 deletions
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2
.github/workflows/main.yml vendored
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@ -23,7 +23,9 @@ 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/
touch /usr/local/bin/test.config
- name: Check ${{ matrix.profile }} profile - name: Check ${{ matrix.profile }} profile
env: env:
SCRATCH: '~' SCRATCH: '~'
NXF_GLOBAL_CONFIG: /usr/local/bin/test.config
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 }}

10
conf/bi.config
View file

@ -1,11 +1,11 @@
params.globalConfig = determine_global_config() params.globalConfig = determine_global_config()
// includeConfig params.globalConfig includeConfig params.globalConfig
def determine_global_config() { def determine_global_config() {
// if( System.getenv('NXF_GLOBAL_CONFIG') == null) if( System.getenv('NXF_GLOBAL_CONFIG') == null)
// { {
// throw new Exception("Environment variable NXF_GLOBAL_CONFIG is missing. Set it to point to global.config file") throw new Exception("Environment variable NXF_GLOBAL_CONFIG is missing. Set it to point to global.config file")
// } }
return System.getenv('NXF_GLOBAL_CONFIG') return System.getenv('NXF_GLOBAL_CONFIG')
} }