diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 43c15cf..5fb2601 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', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] + profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 7f2665e..3011a00 100644 --- a/README.md +++ b/README.md @@ -99,7 +99,8 @@ Currently documentation is available for the following systems: * [BINAC](docs/binac.md) * [CBE](docs/cbe.md) * [CCGA](docs/ccga.md) -* [CCGA_DX](/docs/ccga_dx.md) +* [CCGA_DX](docs/ccga_dx.md) +* [CCGA_MED](docs/ccga_med.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) @@ -126,7 +127,14 @@ Within the local clone of your fork add the custom config file to the [`conf/`]( You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. -Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that. +In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error: + +```bash +Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml +Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML. +set(['']) +##[error]Process completed with exit code 1. +``` Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information. diff --git a/conf/ccga_med.config b/conf/ccga_med.config new file mode 100644 index 0000000..d55fde2 --- /dev/null +++ b/conf/ccga_med.config @@ -0,0 +1,39 @@ +//Profile config names for nf-core/configs +params { + config_profile_description = 'CCGA Med cluster profile provided by nf-core/configs.' + config_profile_contact = 'Marc Hoeppner (@marchoeppner)' + config_profile_url = 'https://www.ccga.uni-kiel.de/' +} + +/* + * ------------------------------------------------- + * Nextflow config file for CCGA cluster in Kiel + * ------------------------------------------------- + */ + +singularity { + enabled = true + runOptions = "-B /work_ifs -B /scratch" + cacheDir = "/work_ifs/ikmb_repository/singularity_cache/" +} + +executor { + queueSize=100 +} + +process { + + // Global process config + executor = 'slurm' + queue = 'all' + +} + +params { + // illumina iGenomes reference file paths on RZCluster + igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/' + saveReference = true + max_memory = 250.GB + max_cpus = 24 + max_time = 120.h +} diff --git a/docs/ccga_med.md b/docs/ccga_med.md new file mode 100644 index 0000000..9aa4236 --- /dev/null +++ b/docs/ccga_med.md @@ -0,0 +1,16 @@ +# nf-core/configs: CCGA Med Cluster Configuration + +Deployment and testing of nf-core pipelines at the CCGA Med cluster is on-going. + +To use, run the pipeline with `-profile ccga_med`. This will download and launch the [`ccga_med.config`](../conf/ccga_med.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on the cluster. You can do this by issuing the commands below: + +```bash +## Load Nextflow and Singularity environment modules +module purge +module load nextflow +module load singularity +``` + +>NB: Access to the CCGA Med cluster is restricted to IKMB/CCGA employees. Please talk to Marc Hoeppner to get access (@marchoeppner). diff --git a/nfcore_custom.config b/nfcore_custom.config index 404d11e..8b4a3a9 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -19,6 +19,7 @@ profiles { cbe { includeConfig "${params.custom_config_base}/conf/cbe.config" } ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" } ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" } + ccga_med { includeConfig "${params.custom_config_base}/conf/ccga_med.config" } cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" } crick { includeConfig "${params.custom_config_base}/conf/crick.config" } czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }