Merge pull request #122 from marchoeppner/ccga-config

Removing old CCGA profile from docs and linting

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          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']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', '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

@@ -97,7 +97,6 @@ Currently documentation is available for the following systems:
 * [BIGPURPLE](docs/bigpurple.md)
 * [BINAC](docs/binac.md)
 * [CBE](docs/cbe.md)
-* [CCGA](docs/ccga.md)
 * [CCGA_DX](docs/ccga_dx.md)
 * [CCGA_MED](docs/ccga_med.md)
 * [CFC](docs/cfc.md)

conf/ccga.config

@@ -1,41 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_description = 'CCGA 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 /ifs -B /scratch -B /work_beegfs"
-  cacheDir = "/ifs/data/nfs_share/ikmb_repository/singularity_cache/"
-}
-
-executor {
-  queueSize=100
-}
-
-process {
-
-  // Global process config
-  executor = 'slurm'
-  queue = 'ikmb_a'
-
-  clusterOptions = { "--qos=ikmb_a" }
-
-}
-
-params {
-  // illumina iGenomes reference file paths on RZCluster
-  igenomes_base = '/ifs/data/nfs_share/ikmb_repository/references/iGenomes/references/'
-  saveReference = true
-  max_memory = 128.GB
-  max_cpus = 16
-  max_time = 120.h
-}

docs/ccga.md

@@ -1,18 +0,0 @@
-# nf-core/configs: CCGA Configuration
-
-Deployment and testing of nf-core pipelines at the CCGA cluster is on-going.
-
-To use, run the pipeline with `-profile ccga`. This will download and launch the [`ccga.config`](../conf/ccga.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 IKMB
-module load Java/1.8.0
-module load Nextflow
-module load singularity3.1.0
-```
-
->NB: Access to the CCGA cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

nfcore_custom.config

@@ -14,7 +14,6 @@ profiles {
   bigpurple    { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
   binac        { includeConfig "${params.custom_config_base}/conf/binac.config" }
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
-  ccga         { includeConfig "${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" }