From cdbdbee0eb98d586b37f8e560d092c1bcfc2593d Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 5 Dec 2019 11:49:44 +0100
Subject: [PATCH] replace -profile uppmax_devel by -profile uppmax,devel

---
 .github/workflows/main.yml |  2 +-
 README.md                  |  1 -
 conf/uppmax.config         | 14 ++++++++++++++
 conf/uppmax_devel.config   | 21 ---------------------
 docs/uppmax.md             |  4 ++--
 5 files changed, 17 insertions(+), 25 deletions(-)
 delete mode 100644 conf/uppmax_devel.config

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7d78a45..082fec5 100644
--- a/.github/workflows/main.yml
+++ b/.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
diff --git a/README.md b/README.md
index 8709e2a..098eea8 100644
--- a/README.md
+++ b/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`
diff --git a/conf/uppmax.config b/conf/uppmax.config
index d2fbc5d..89efd48 100644
--- a/conf/uppmax.config
+++ b/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'
+  }
+}
\ No newline at end of file
diff --git a/conf/uppmax_devel.config b/conf/uppmax_devel.config
deleted file mode 100644
index ad71ac4..0000000
--- a/conf/uppmax_devel.config
+++ /dev/null
@@ -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
-}
diff --git a/docs/uppmax.md b/docs/uppmax.md
index 4c58e9b..25a8867 100644
--- a/docs/uppmax.md
+++ b/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`.