1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-10 20:13:09 +00:00

Documentation tweaks

This commit is contained in:
Phil Ewels 2019-01-07 14:25:06 +01:00
parent 723428c186
commit 66a08891c7
12 changed files with 65 additions and 30 deletions

View file

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

View file

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

View file

@ -1,7 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'CFC' 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_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'http://qbic.uni-tuebingen.de/' config_profile_url = 'http://qbic.uni-tuebingen.de/'
} }

View file

@ -1,7 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'CRICK' 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_contact = 'Harshil Patel (@drpatelh )'
config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies'
} }

View file

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

View file

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

View file

@ -1,7 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'PHOENIX' 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_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
config_profile_url = 'https://www.adelaide.edu.au/phoenix/' config_profile_url = 'https://www.adelaide.edu.au/phoenix/'
} }

View file

@ -1,7 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'SHH' 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_contact = 'James Fellows Yates (@jfy133)'
config_profile_url = 'https://shh.mpg.de' config_profile_url = 'https://shh.mpg.de'
} }

View file

@ -1,20 +1,11 @@
//Profile config names for nf-core/configs // Profile config names for nf-core/configs
params { 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_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'https://www.uppmax.uu.se/' 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 { executor {
name = 'slurm' name = 'slurm'
queueSize = 1 queueSize = 1

View file

@ -1,17 +1,11 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'UPPMAX' 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_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'https://www.uppmax.uu.se/' 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 { singularity {
enabled = true enabled = true
} }
@ -23,8 +17,7 @@ process {
params { params {
saveReference = true 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_memory = 128.GB
max_cpus = 16 max_cpus = 16
max_time = 240.h max_time = 240.h

View file

@ -1,6 +1,6 @@
# nf-core/configs: BINAC Configuration # 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. 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.

51
docs/uppmax.md Normal file
View file

@ -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`.