Merge pull request #118 from marchoeppner/ccga-config

Adding new CCGA Med Cluster to profiles

.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

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(['<profile_name>'])
+##[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.
 

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
+}

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).

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" }