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update docs for munin/sarek specific config

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MaxUlysse 2020-03-11 14:17:24 +01:00
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docs/pipeline/sarek/munin.md
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@ -6,17 +6,22 @@ Extra specific configuration for sarek pipeline
To use, run the pipeline with `-profile munin`.
This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster.
This will download and launch the sarek specific [`munin.config`](../../../conf/pipeline/sarek/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
Example: `nextflow run nf-core/sarek -profile munin`
## Sarek specific configurations for MUNIN
Specific configurations for MUNIN has been made for sarek.
Specific configurations for `MUNIN` has been made for sarek.
* Params `annotation_cache` set to `true`
* Path to `snpEff_cache`: `/data1/cache/snpEff/`
* Params `annotation_cache` and `cadd_cache` set to `true`
* Params `vep_cache_version` set to `95`
* Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
* Load module `Sentieon` for Processes with `sentieon` labels