From 66a08891c7630f01a80f2707d0d62c3febc41fb3 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 7 Jan 2019 14:25:06 +0100 Subject: [PATCH] Documentation tweaks --- conf/binac.config | 2 +- conf/ccga.config | 2 +- conf/cfc.config | 2 +- conf/crick.config | 2 +- conf/hebbe.config | 2 +- conf/mendel.config | 2 +- conf/phoenix.config | 2 +- conf/shh.config | 2 +- conf/uppmax-devel.config | 15 +++--------- conf/uppmax.config | 11 ++------- docs/binac.md | 2 +- docs/uppmax.md | 51 ++++++++++++++++++++++++++++++++++++++++ 12 files changed, 65 insertions(+), 30 deletions(-) create mode 100644 docs/uppmax.md diff --git a/conf/binac.config b/conf/binac.config index d256e5a..cde5218 100644 --- a/conf/binac.config +++ b/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' } diff --git a/conf/ccga.config b/conf/ccga.config index 2e83ae2..7dff7c7 100644 --- a/conf/ccga.config +++ b/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/' } diff --git a/conf/cfc.config b/conf/cfc.config index ee7943d..9c39fd5 100644 --- a/conf/cfc.config +++ b/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/' } diff --git a/conf/crick.config b/conf/crick.config index 02a835d..de8c89b 100755 --- a/conf/crick.config +++ b/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' } diff --git a/conf/hebbe.config b/conf/hebbe.config index 9187a85..76b8ac7 100644 --- a/conf/hebbe.config +++ b/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' } diff --git a/conf/mendel.config b/conf/mendel.config index ec076c7..ca0d784 100644 --- a/conf/mendel.config +++ b/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/' } diff --git a/conf/phoenix.config b/conf/phoenix.config index 2987021..685e1e5 100644 --- a/conf/phoenix.config +++ b/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/' } diff --git a/conf/shh.config b/conf/shh.config index 1410b3a..23f1e00 100644 --- a/conf/shh.config +++ b/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' } diff --git a/conf/uppmax-devel.config b/conf/uppmax-devel.config index 6de50ed..760ff77 100644 --- a/conf/uppmax-devel.config +++ b/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_description = 'UPPMAX Development Cluster Profile provided by nf-core/configs.' + config_profile_name = 'UPPMAX-devel' + 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 diff --git a/conf/uppmax.config b/conf/uppmax.config index 2442669..939b8a7 100644 --- a/conf/uppmax.config +++ b/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 diff --git a/docs/binac.md b/docs/binac.md index e7c6fbd..c67894e 100644 --- a/docs/binac.md +++ b/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. diff --git a/docs/uppmax.md b/docs/uppmax.md new file mode 100644 index 0000000..6598792 --- /dev/null +++ b/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 ` 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`.