Adding new CCGA Med Cluster to profiles

Updating README and fixing linting errors in CCGA_MED profile

Fixing order in profile queue and removed leading slash from readme for ccga profile docs

Fixing order in profile queue and removed leading slash from readme for ccga profile docs

.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 +127,13 @@ 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" }