replace -profile uppmax_devel by -profile uppmax,devel

.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_sdag', 'shh_cdag', 'uct_hex', 'uppmax_devel', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh_sdag', 'shh_cdag', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -117,7 +117,6 @@ Currently documentation is available for the following systems:
 * [SHH](docs/shh.md)
 * [UCT_HEX](docs/uct_hex.md)
 * [UPPMAX](docs/uppmax.md)
-* [UPPMAX_DEVEL](docs/uppmax.md)
 * [UZH](docs/uzh.md)
 
 ### Uploading to `nf-core/configs`

conf/uppmax.config

@@ -7,6 +7,7 @@ params {
 
 singularity {
   enabled = true
+  cacheDir = '/sw/data/uppnex/ToolBox/nf-core'
 }
 
 process {
@@ -23,3 +24,16 @@ params {
   // illumina iGenomes reference file paths on UPPMAX
   igenomes_base = '/sw/data/uppnex/igenomes/'
 }
+
+profiles {
+  devel {
+    params {
+      config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
+      // Max resources to be requested by a devel job
+      max_memory = 120.GB
+      max_time = 1.h
+    }
+    executor.queueSize = 1
+    process.queue = 'devel'
+  }
+}

conf/uppmax_devel.config

@@ -1,21 +0,0 @@
-// Profile config names for nf-core/configs
-params {
-  config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
-  config_profile_contact = 'Phil Ewels (@ewels)'
-  config_profile_url = 'https://www.uppmax.uu.se/'
-}
-
-executor {
-  name = 'slurm'
-  queueSize = 1
-}
-process {
-  queue = 'devel'
-}
-
-params {
-  // Max resources to be requested by a devel job
-  max_memory = 120.GB
-  max_cpus = 16
-  max_time = 1.h
-}

docs/uppmax.md

@@ -50,7 +50,7 @@ Note that each job will still start with the same request as normal, but restart
 
 All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
 
-## Uppmax-devel config
+## devel config
 
 If doing pipeline development work on Uppmax, this profile allows for faster testing.
 
@@ -59,4 +59,4 @@ Applied after main UPPMAX config, it overwrites certain parts of the config and
 All jobs are limited to 1 hour to be eligible for this queue and only one job allowed at a time.
 It is not suitable for use with real data.
 
-To use it, submit with `-profile uppmax-devel`.
+To use it, submit with `-profile uppmax,devel`.