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https://github.com/MillironX/nf-configs.git
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commit
9497b78149
6 changed files with 49 additions and 42 deletions
2
.github/workflows/main.yml
vendored
2
.github/workflows/main.yml
vendored
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@ -16,7 +16,7 @@ jobs:
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needs: test_all_profiles
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strategy:
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matrix:
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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']
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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']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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@ -117,7 +117,6 @@ Currently documentation is available for the following systems:
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* [SHH](docs/shh.md)
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* [UCT_HEX](docs/uct_hex.md)
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* [UPPMAX](docs/uppmax.md)
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* [UPPMAX_DEVEL](docs/uppmax.md)
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* [UZH](docs/uzh.md)
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### Uploading to `nf-core/configs`
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@ -17,9 +17,36 @@ process {
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params {
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saveReference = true
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max_memory = 128.GB
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max_memory = 125.GB
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max_cpus = 16
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max_time = 240.h
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// illumina iGenomes reference file paths on UPPMAX
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igenomes_base = '/sw/data/uppnex/igenomes/'
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}
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def hostname = "hostname".execute().text.trim()
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if (hostname ==~ "b.*") {
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params.max_memory = 109.GB
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}
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if (hostname ==~ "i.*") {
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params.max_memory = 250.GB
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}
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if (hostname ==~ "r.*") {
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params.max_cpus = 20
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}
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profiles {
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devel {
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params {
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config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
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// Max resources to be requested by a devel job
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max_memory = 120.GB
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max_time = 1.h
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}
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executor.queueSize = 1
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process.queue = 'devel'
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}
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}
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@ -1,21 +0,0 @@
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// Profile config names for nf-core/configs
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params {
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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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executor {
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name = 'slurm'
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queueSize = 1
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}
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process {
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queue = 'devel'
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}
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params {
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// Max resources to be requested by a devel job
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max_memory = 120.GB
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max_cpus = 16
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max_time = 1.h
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}
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@ -4,7 +4,9 @@ All nf-core pipelines have been successfully configured for use on the Swedish U
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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, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
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To use, run the pipeline with `-profile uppmax` (one hyphen).
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This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
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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.
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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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@ -23,18 +25,6 @@ Just run Nextflow on a login node and it will handle everything else.
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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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Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited:
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```bash
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--max_memory "112GB"
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```
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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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@ -50,13 +40,27 @@ Note that each job will still start with the same request as normal, but restart
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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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## How to specify a UPPMAX cluster
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If doing pipeline development work on Uppmax, this profile allows for faster testing.
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The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
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* `bianca`
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* cpus available: 16 cpus
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* memory available: 109 GB
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* `irma`
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* cpus available: 16 cpus
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* memory available: 250 GB
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* `rackham`
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* cpus available: 20 cpus
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* memory available: 125 GB
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## Development config
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If doing pipeline development work on UPPMAX, the `devel` 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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To use it, submit with `-profile uppmax,devel`.
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@ -38,8 +38,6 @@ profiles {
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shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
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uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
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uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
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uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config";
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includeConfig "${params.custom_config_base}/conf/uppmax_devel.config" }
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uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
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}
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