diff --git a/README.md b/README.md index 18d8edbf..445467b 100644 --- a/README.md +++ b/README.md @@ -207,6 +207,7 @@ Currently documentation is available for the following pipelines within specific - rnavar - [MUNIN](docs/pipeline/rnavar/munin.md) - sarek + - [Cancer Research UK Manchester Institute](docs/pipeline/sarek/crukmi.md) - [MUNIN](docs/pipeline/sarek/munin.md) - [UPPMAX](docs/pipeline/sarek/uppmax.md) - taxprofiler diff --git a/docs/pipeline/sarek/crukmi.md b/docs/pipeline/sarek/crukmi.md new file mode 100644 index 0000000..01d030a --- /dev/null +++ b/docs/pipeline/sarek/crukmi.md @@ -0,0 +1,17 @@ +# nf-core/configs: CRUK-MI sarek specific configuration + +Extra specific configuration for sarek pipeline + +## Usage + +To use, run the pipeline with `-profile crukmi`. + +This will download and launch the sarek specific [`crukmi.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the Cancer Research UK Manchester Institute cluster (phoenix). + +Example: `nextflow run nf-core/sarek -profile crukmi` + +## Sarek specific configurations for CRUK-MI + +Specific configurations for `CRUK-MI` has been made for sarek. + +- Initial requested resources for SAMTOOLS_MPILEUP are only 5GB and 1 core.