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Merge pull request #155 from piotr-faba-ardigen/add_bi_config

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Add BI internal config
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Alexander Peltzer 2020-05-27 17:49:41 +02:00 committed by GitHub
commit 27f3207cb9
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3 changed files with 19 additions and 1 deletions
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3
.github/workflows/main.yml vendored
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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles needs: test_all_profiles
strategy: strategy:
matrix: matrix:
profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh']
steps: steps:
- uses: actions/checkout@v1 - uses: actions/checkout@v1
- name: Install Nextflow - name: Install Nextflow
@ -26,4 +26,5 @@ jobs:
- name: Check ${{ matrix.profile }} profile - name: Check ${{ matrix.profile }} profile
env: env:
SCRATCH: '~' SCRATCH: '~'
NXF_GLOBAL_CONFIG: awsbatch.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 }}

16
conf/bi.config Normal file
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@ -0,0 +1,16 @@
params{
config_profile_description = 'Boehringer Ingelheim internal profile provided by nf-core/configs.'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'https://www.boehringer-ingelheim.com/'
}
params.globalConfig = determine_global_config()
includeConfig params.globalConfig
def determine_global_config() {
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")
}
return System.getenv('NXF_GLOBAL_CONFIG')
}

1
nfcore_custom.config
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@ -11,6 +11,7 @@
//Please use a new line per include Config section to allow easier linting/parsing. Thank you. //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
profiles { profiles {
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" } awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
binac { includeConfig "${params.custom_config_base}/conf/binac.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }