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nf-configs/docs/pipeline/sarek/munin.md
MaxUlysse 7c60096952 update docs for munin/sarek specific config
2020-03-11 14:17:24 +01:00

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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 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