Merge branch 'master' into master

.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_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', '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/cbe.config

@@ -7,7 +7,7 @@ params {
 
 process {
   executor = 'slurm'
-  module = 'singularity/3.2.1'
+  module = 'singularity/3.4.1'
   queue = { task.memory <= 170.GB ? 'c' : 'm' }
   clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
 }

conf/uppmax.config

@@ -17,9 +17,36 @@ process {
 params {
   saveReference = true
 
-  max_memory = 128.GB
+  max_memory = 125.GB
   max_cpus = 16
   max_time = 240.h
   // illumina iGenomes reference file paths on UPPMAX
   igenomes_base = '/sw/data/uppnex/igenomes/'
 }
+
+def hostname = "hostname".execute().text.trim()
+
+if (hostname ==~ "b.*") {
+  params.max_memory = 109.GB
+}
+
+if (hostname ==~ "i.*") {
+  params.max_memory = 250.GB
+}
+
+if (hostname ==~ "r.*") {
+  params.max_cpus = 20
+}
+
+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

@@ -4,7 +4,9 @@ All nf-core pipelines have been successfully configured for use on the Swedish U
 
 ## Using the UPPMAX config profile
 
-To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. 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.
+To use, run the pipeline with `-profile uppmax` (one hyphen).
+This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
+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.
 
 In addition to this config profile, you will also need to specify an UPPMAX project id.
 You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
@@ -23,18 +25,6 @@ Just run Nextflow on a login node and it will handle everything else.
 A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`.
 You can do this by simply using the `--genome <GENOME_ID>` parameter.
 
-## Running offline with Bianca
-
-If running on Bianca, you will have no internet connection and these configs will not be loaded.
-Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca.
-This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available.
-
-Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited:
-
-```bash
---max_memory "112GB"
-```
-
 ## Getting more memory
 
 If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags:
@@ -50,13 +40,27 @@ 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
+## How to specify a UPPMAX cluster
 
-If doing pipeline development work on Uppmax, this profile allows for faster testing.
+The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
+
+* `bianca`
+  * cpus available: 16 cpus
+  * memory available: 109 GB
+* `irma`
+  * cpus available: 16 cpus
+  * memory available: 250 GB
+* `rackham`
+  * cpus available: 20 cpus
+  * memory available: 125 GB
+
+## Development config
+
+If doing pipeline development work on UPPMAX, the `devel` profile allows for faster testing.
 
 Applied after main UPPMAX config, it overwrites certain parts of the config and submits jobs to the `devcore` queue, which has much faster queue times.
 
 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`.

nfcore_custom.config

@@ -38,8 +38,6 @@ profiles {
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hex      { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
-  uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; 
-                 includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }
 }
 
@@ -49,6 +47,7 @@ profiles {
 params {
   // This is a groovy map, not a nextflow parameter set
   hostnames = [
+    cbe: ['.cbe.vbc.ac.at'],
     crick: ['.thecrick.org'],
     genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
     genouest: ['.genouest.org'],