mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-14 13:43:09 +00:00
27 lines
1.1 KiB
Markdown
27 lines
1.1 KiB
Markdown
# nf-core/configs: MUNIN sarek specific configuration
|
|
|
|
Extra specific configuration for sarek pipeline
|
|
|
|
## Usage
|
|
|
|
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.
|
|
|
|
Example: `nextflow run nf-core/sarek -profile munin`
|
|
|
|
## Sarek specific configurations for MUNIN
|
|
|
|
Specific configurations for `MUNIN` has been made for sarek.
|
|
|
|
* 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
|