From 1354ae40635dbf130f92df22d93a01e70b07c745 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:19:15 +0200 Subject: [PATCH 01/11] 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" } From c31b03108c4308c70a6f4ac68840ad0cbe37e308 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:22:56 +0200 Subject: [PATCH 02/11] retry without Exception --- conf/bi.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/bi.config b/conf/bi.config index 874d9f8..091092c 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -3,9 +3,9 @@ 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") - } + // 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') } From 2685275952076be368b7103b0f49bf11f2ed1aac Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:24:47 +0200 Subject: [PATCH 03/11] switch include off --- conf/bi.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/bi.config b/conf/bi.config index 091092c..6fa20d6 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -1,6 +1,6 @@ params.globalConfig = determine_global_config() -includeConfig params.globalConfig +// includeConfig params.globalConfig def determine_global_config() { // if( System.getenv('NXF_GLOBAL_CONFIG') == null) From 66f191a1cfd87ac5b5b728a0ebc73b84b9d469c9 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:30:00 +0200 Subject: [PATCH 04/11] declate NXF_GLOBAL_CONFIG in ci --- .github/workflows/main.yml | 2 ++ conf/bi.config | 10 +++++----- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index b927957..8226dac 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,7 +23,9 @@ jobs: run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ + touch /usr/local/bin/test.config - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' + NXF_GLOBAL_CONFIG: /usr/local/bin/test.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} diff --git a/conf/bi.config b/conf/bi.config index 6fa20d6..874d9f8 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -1,11 +1,11 @@ params.globalConfig = determine_global_config() -// includeConfig params.globalConfig +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") - // } + 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') } From ab3070582e94ded2270dcacd69b1348aceec488f Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:32:19 +0200 Subject: [PATCH 05/11] Fix paths to dummy.config --- .github/workflows/main.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8226dac..8c6d23b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,9 +23,9 @@ jobs: run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - touch /usr/local/bin/test.config + touch ~/dummy.config - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' - NXF_GLOBAL_CONFIG: /usr/local/bin/test.config + NXF_GLOBAL_CONFIG: ~/dummy.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} From ff5fdd097bf418b1cb78a7a171c1fb9a4744ee59 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:35:55 +0200 Subject: [PATCH 06/11] debug --- .github/workflows/main.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8c6d23b..d4e0232 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,9 +23,13 @@ jobs: run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ + echo ~ touch ~/dummy.config - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' NXF_GLOBAL_CONFIG: ~/dummy.config - run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} + run: | + echo $SCRATCH + echo $NXF_GLOBAL_CONFIG + nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} From ac47d020cb8f09dac8ceae1ca3e2f86c3ed591f7 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:38:11 +0200 Subject: [PATCH 07/11] debug: continue --- .github/workflows/main.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d4e0232..8c50e7a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,12 +23,11 @@ jobs: run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - echo ~ - touch ~/dummy.config + touch /home/runner/dummy.config - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' - NXF_GLOBAL_CONFIG: ~/dummy.config + NXF_GLOBAL_CONFIG: /home/runner/dummy.config run: | echo $SCRATCH echo $NXF_GLOBAL_CONFIG From 1a9db371c380e4c1a044a3586bb33ac492f714bd Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:43:32 +0200 Subject: [PATCH 08/11] remove echos --- .github/workflows/main.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 8c50e7a..c906cf9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -28,7 +28,4 @@ jobs: env: SCRATCH: '~' NXF_GLOBAL_CONFIG: /home/runner/dummy.config - run: | - echo $SCRATCH - echo $NXF_GLOBAL_CONFIG - 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 }} From 3ad0003979a4d7c598be03980d1640c9327a8478 Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:46:08 +0200 Subject: [PATCH 09/11] test without dummy config --- .github/workflows/main.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index c906cf9..0742e5c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,9 +23,8 @@ jobs: run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - touch /home/runner/dummy.config - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' - NXF_GLOBAL_CONFIG: /home/runner/dummy.config + NXF_GLOBAL_CONFIG: ${GITHUB_WORKSPACE}/config/awsbatch.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} From f5e2a9f9f3443ae4be1885cd816ae0bc62cc27fc Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 16:55:37 +0200 Subject: [PATCH 10/11] try without dummy.config: use relative path --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 0742e5c..0609a85 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -26,5 +26,5 @@ jobs: - name: Check ${{ matrix.profile }} profile env: SCRATCH: '~' - NXF_GLOBAL_CONFIG: ${GITHUB_WORKSPACE}/config/awsbatch.config + NXF_GLOBAL_CONFIG: awsbatch.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} From 18d8edb0469c81838ddd4454b2d410b3807fe1cc Mon Sep 17 00:00:00 2001 From: Piotr Faba Date: Wed, 27 May 2020 17:41:19 +0200 Subject: [PATCH 11/11] add description and profile --- conf/bi.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/bi.config b/conf/bi.config index 874d9f8..0ad15d4 100644 --- a/conf/bi.config +++ b/conf/bi.config @@ -1,3 +1,8 @@ +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