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update readme
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sorelfitzgibbon committed Dec 18, 2024
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*Providing `intersect_regions` is required and will limit the final output to just those regions. All regions of the reference genome could be provided as a `bed` file with all contigs, however it is HIGHLY recommended to remove `decoy` contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for `Mutect2` and will cause a very long runtime for `Strelka2`. See [Discussion here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216). For `uclahs-cds` users, a GRCh38 `bed.gz` file can be found here: `/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz`.

### Base resource allocation updaters
To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the [input.config](config/template.config) file. The default allocations can be found in `config/resources.json`. If available resources have matched cpus and memory within `90% - 1GB` of one of the pre-specified configurations, that configuration will be used. Otherwise the default configuration will be used. A spreadsheet view of the resource configuration as of Dec 2024 is [here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/328)
To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the [input.config](config/template.config) file. The default allocations can be found in `config/resources.json`. If available resources have matched cpus and memory within `90% - 1GB` of one of the pre-specified configurations, that configuration will be used. Otherwise the default configuration will be used. A spreadsheet view of the resource configuration as of Dec 2024 is [here](https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/328). For very large or challanging input samples, we suggest using the `m64` configuration or similar.


```Nextflow
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