From 1354ae40635dbf130f92df22d93a01e70b07c745 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:19:15 +0200 Subject: [PATCH] add bi config --- .github/workflows/main.yml | 2 +- conf/bi.config | 11 +++++++++++ nfcore_custom.config | 1 + 3 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 conf/bi.config diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index bdc485b..b927957 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: 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: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/conf/bi.config b/conf/bi.config new file mode 100644 index 0000000..874d9f8 --- /dev/null +++ b/conf/bi.config @@ -0,0 +1,11 @@ +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') +} diff --git a/nfcore_custom.config b/nfcore_custom.config index ea2238a..3f89d83 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -11,6 +11,7 @@ //Please use a new line per include Config section to allow easier linting/parsing. Thank you. profiles { awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" } + bi { includeConfig "${params.custom_config_base}/conf/bi.config" } bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" } binac { includeConfig "${params.custom_config_base}/conf/binac.config" } cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" }