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update docs
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2 changed files with 23 additions and 19 deletions
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@ -27,10 +27,6 @@ params {
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def hostname = "hostname".execute().text.trim()
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def hostname = "hostname".execute().text.trim()
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if (hostname ==~ "r.*") {
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params.max_cpus = 20
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}
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if (hostname ==~ "b.*") {
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if (hostname ==~ "b.*") {
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params.max_memory = 109.GB
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params.max_memory = 109.GB
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}
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}
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@ -39,6 +35,10 @@ if (hostname ==~ "i.*") {
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params.max_memory = 250.GB
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params.max_memory = 250.GB
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}
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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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profiles {
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devel {
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devel {
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params {
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params {
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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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## 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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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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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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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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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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## 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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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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@ -50,9 +40,23 @@ 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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All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
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## 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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You actually do not need to, based on `hostnames`, configuration will be automatically applied for the cluster you are on following these specifications:
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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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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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