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Merge pull request #155 from piotr-faba-ardigen/add_bi_config
Add BI internal config
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commit
27f3207cb9
3 changed files with 19 additions and 1 deletions
3
.github/workflows/main.yml
vendored
3
.github/workflows/main.yml
vendored
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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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']
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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']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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@ -26,4 +26,5 @@ jobs:
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- name: Check ${{ matrix.profile }} profile
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env:
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SCRATCH: '~'
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NXF_GLOBAL_CONFIG: awsbatch.config
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run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
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16
conf/bi.config
Normal file
16
conf/bi.config
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@ -0,0 +1,16 @@
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params{
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config_profile_description = 'Boehringer Ingelheim internal profile provided by nf-core/configs.'
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_url = 'https://www.boehringer-ingelheim.com/'
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}
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params.globalConfig = determine_global_config()
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includeConfig params.globalConfig
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def determine_global_config() {
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if( System.getenv('NXF_GLOBAL_CONFIG') == null)
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{
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throw new Exception("Environment variable NXF_GLOBAL_CONFIG is missing. Set it to point to global.config file")
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}
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return System.getenv('NXF_GLOBAL_CONFIG')
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}
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@ -11,6 +11,7 @@
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//Please use a new line per include Config section to allow easier linting/parsing. Thank you.
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profiles {
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awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
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bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
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bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
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binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
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cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }
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