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Documentation tweaks
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Phil Ewels
parent
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66a08891c7
12 changed files with 65 additions and 30 deletions
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'BINAC'
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config_profile_description = 'BINAC Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'BINAC cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'CCGA'
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config_profile_description = 'CCGA Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
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config_profile_url = 'https://www.ikmb.uni-kiel.de/'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'CFC'
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config_profile_description = 'Core Facility Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Alexander Peltzer (@apeltzer)'
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config_profile_url = 'http://qbic.uni-tuebingen.de/'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'CRICK'
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config_profile_description = 'The Francis Crick Institute CAMP HPC Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Harshil Patel (@drpatelh )'
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config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'HEBBE'
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config_profile_description = 'Gothenburg Hebbe Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Phil Ewels (@ewels )'
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config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'MENDEL'
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config_profile_description = 'MENDEL cluster profile provided by nf-core/configs'
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config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs'
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config_profile_contact = 'Philipp H (@phue)'
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config_profile_url = 'http://www.gmi.oeaw.ac.at/'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'PHOENIX'
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config_profile_description = 'Phoenix Research cluster profile provided by nf-core/configs'
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config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs'
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config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
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config_profile_url = 'https://www.adelaide.edu.au/phoenix/'
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}
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'SHH'
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config_profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.'
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config_profile_contact = 'James Fellows Yates (@jfy133)'
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config_profile_url = 'https://shh.mpg.de'
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}
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//Profile config names for nf-core/configs
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// Profile config names for nf-core/configs
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params {
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config_profile_name = 'UPPMAX-DEVEL'
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config_profile_description = 'UPPMAX Development Cluster Profile provided by nf-core/configs.'
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config_profile_name = 'UPPMAX-devel'
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config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
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config_profile_contact = 'Phil Ewels (@ewels)'
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config_profile_url = 'https://www.uppmax.uu.se/'
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}
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/* Additional description:
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* To be applied after main UPPMAX config, overwrites config and
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* submits jobs to the `devcore` queue, which has much faster
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* queue times. All jobs are limited to 1 hour to be eligible
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* for this queue and only one job allowed at a time.
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*/
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executor {
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name = 'slurm'
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queueSize = 1
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//Profile config names for nf-core/configs
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params {
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config_profile_name = 'UPPMAX'
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config_profile_description = 'UPPMAX Cluster Profile provided by nf-core/configs.'
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config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.'
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config_profile_contact = 'Phil Ewels (@ewels)'
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config_profile_url = 'https://www.uppmax.uu.se/'
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}
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/* Additional description:
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* Defines reference genomes, using iGenome paths
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* Imported under the default 'standard' Nextflow
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* profile in nextflow.config
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*/
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singularity {
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enabled = true
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}
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@ -23,8 +17,7 @@ process {
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params {
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saveReference = true
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// Max resources requested by a normal node on milou. If you need more memory, run on a fat node using:
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// --clusterOptions "-C mem512GB" --max_memory "512GB"
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max_memory = 128.GB
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max_cpus = 16
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max_time = 240.h
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# nf-core/configs: BINAC Configuration
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All nf-core pipelines have been successfully configured for use on the BINAC cluster at the insert institution here.
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All nf-core pipelines have been successfully configured for use on the BinAC cluster at Baden-Württemberg HPC.
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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.
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51
docs/uppmax.md
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51
docs/uppmax.md
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# nf-core/configs: UPPMAX Configuration
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All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
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## Using the UPPMAX config profile
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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.
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In addition to this config profile, you will also need to specify an UPPMAX project id.
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You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
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```bash
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nextflow run nf-core/PIPELINE -profile uppmax --project SNIC 2018/1-234 # ..rest of pipeline flags
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```
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Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
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This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler.
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Just run Nextflow on a login node and it will handle everything else.
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## Using iGenomes references
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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`.
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You can do this by simply using the `--genome <GENOME_ID>` parameter.
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## Running offline with Bianca
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If running on Bianca, you will have no internet connection and these configs will not be loaded.
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Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca.
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This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available.
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## Getting more memory
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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:
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```bash
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--clusterOptions "-C mem256GB" --max_memory "256GB"
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```
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This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
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Rackham has nodes with 128GB, 256GB and 1TB memory available.
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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.
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All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
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## Uppmax-devel config
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If doing pipeline development work on Uppmax, this profile allows for faster testing.
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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.
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All jobs are limited to 1 hour to be eligible for this queue and only one job allowed at a time.
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It is not suitable for use with real data.
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To use it, submit with `-profile uppmax-devel`.
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