millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 08:29:54 +00:00
Code Issues Releases Packages Activity

declate NXF_GLOBAL_CONFIG in ci

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

2
.github/workflows/main.yml vendored
View file

@ -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')
} }