feat: remove kraken profile

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -116,7 +116,6 @@ Currently documentation is available for the following systems:
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
-* [KRAKEN](docs/kraken.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
 * [OIST](docs/oist.md)

conf/kraken.config

@@ -1,24 +0,0 @@
-//Profile config names for nf-core/configs
-params {
-  config_profile_name = 'KRAKEN'
-  config_profile_description = 'Jenkins cluster provided by nf-core/configs.'
-  config_profile_contact = 'Maxime Garcia or Johannes Alneberg'
-  config_profile_url = 'kraken.dyn.scilifelab.se'
-}
-
-process {
-  executor = 'local'
-}
-
-docker {
-  enabled = true
-  mountFlags = 'z'
-  fixOwnership = true
-}
-
-params {
-  max_memory = 60.GB
-  max_cpus = 16
-  max_time = 72.h
-  igenomes_base = '/share/igenomes/'
-}

docs/kraken.md

@@ -1,10 +0,0 @@
-# nf-core/configs: KRAKEN Configuration
-
-This profile can be **only** combined with `jenkins.config`. It is used for
-testing pipeline with real data on **in-house** cluster located at SciLifeLab.
-
-To use, run the pipeline with `-profile kraken`. This will download and launch
-the [`kraken.config`](../conf/kraken.config) which has been pre-configured to
-test the pipeline using `docker` by default.
-
-Example: `nextflow run -profile kraken,jenkins`

nfcore_custom.config

@@ -36,7 +36,6 @@ profiles {
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
-  kraken       { includeConfig "${params.custom_config_base}/conf/kraken.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   oist         { includeConfig "${params.custom_config_base}/conf/oist.config" }