Documentation tweaks

conf/binac.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'BINAC'
-  config_profile_description = 'BINAC Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'BINAC cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Alexander Peltzer (@apeltzer)'
   config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC'
 }

conf/ccga.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'CCGA'
-  config_profile_description = 'CCGA Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
   config_profile_url = 'https://www.ikmb.uni-kiel.de/'
 }

conf/cfc.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'CFC'
-  config_profile_description = 'Core Facility Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Alexander Peltzer (@apeltzer)'
   config_profile_url = 'http://qbic.uni-tuebingen.de/'
 }

conf/crick.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'CRICK'
-  config_profile_description = 'The Francis Crick Institute CAMP HPC Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Harshil Patel (@drpatelh )'
   config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies'
 }

conf/hebbe.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'HEBBE'
-  config_profile_description = 'Gothenburg Hebbe Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Phil Ewels (@ewels )'
   config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe'
 }

conf/mendel.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'MENDEL'
-  config_profile_description = 'MENDEL cluster profile provided by nf-core/configs'
+  config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs'
   config_profile_contact = 'Philipp H (@phue)'
   config_profile_url = 'http://www.gmi.oeaw.ac.at/'
 }

conf/phoenix.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'PHOENIX'
-  config_profile_description = 'Phoenix Research cluster profile provided by nf-core/configs'
+  config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs'
   config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
   config_profile_url = 'https://www.adelaide.edu.au/phoenix/'
 }

conf/shh.config

@@ -1,7 +1,7 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'SHH'
-  config_profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.'
   config_profile_contact = 'James Fellows Yates (@jfy133)'
   config_profile_url = 'https://shh.mpg.de'
 }

conf/uppmax-devel.config

@@ -1,20 +1,11 @@
-//Profile config names for nf-core/configs
+// Profile config names for nf-core/configs
 params {
-  config_profile_name = 'UPPMAX-DEVEL'
+  config_profile_name = 'UPPMAX-devel'
-  config_profile_description = 'UPPMAX Development Cluster Profile provided by nf-core/configs.'
+  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/'
 }
 
-/* Additional description:
- * To be applied after main UPPMAX config, overwrites 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.
- */
-
-
-
 executor {
   name = 'slurm'
   queueSize = 1

conf/uppmax.config

@@ -1,17 +1,11 @@
 //Profile config names for nf-core/configs
 params {
   config_profile_name = 'UPPMAX'
-  config_profile_description = 'UPPMAX Cluster Profile provided by nf-core/configs.'
+  config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.'
   config_profile_contact = 'Phil Ewels (@ewels)'
   config_profile_url = 'https://www.uppmax.uu.se/'
 }
 
-/* Additional description:
- * Defines reference genomes, using iGenome paths
- * Imported under the default 'standard' Nextflow
- * profile in nextflow.config
- */
-
 singularity {
   enabled = true
 }
@@ -23,8 +17,7 @@ process {
 
 params {
   saveReference = true
-  // Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
+
-  //   --clusterOptions "-C mem512GB" --max_memory "512GB"
   max_memory = 128.GB
   max_cpus = 16
   max_time = 240.h

docs/binac.md

@@ -1,6 +1,6 @@
 # nf-core/configs: BINAC Configuration
 
-All nf-core pipelines have been successfully configured for use on the BINAC cluster at the insert institution here.
+All nf-core pipelines have been successfully configured for use on the BinAC cluster at Baden-Württemberg HPC.
 
 To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline.
 

docs/uppmax.md

@@ -0,0 +1,51 @@
+# nf-core/configs: UPPMAX Configuration
+
+All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
+
+## 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, Nextflow will download a singularity image with all of the required software 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:
+
+```bash
+nextflow run nf-core/PIPELINE -profile uppmax --project SNIC 2018/1-234 # ..rest of pipeline flags
+```
+
+Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
+
+This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler.
+Just run Nextflow on a login node and it will handle everything else.
+
+## Using iGenomes references
+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.
+
+## 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:
+
+```bash
+--clusterOptions "-C mem256GB" --max_memory "256GB"
+```
+
+This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
+Rackham has nodes with 128GB, 256GB and 1TB memory available.
+
+Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory.
+
+All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
+
+## Uppmax-devel config
+If doing pipeline development work on Uppmax, this 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`.