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nf-configs/docs/pipeline/rnavar/munin.md
praveenraj2018 00a3ed0fa6
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nf-core/configs: MUNIN rnavar specific configuration

Extra specific configuration for rnavar pipeline

Usage

To use, run the pipeline with -profile munin.

This will download and launch the rnavar specific munin.config which has been pre-configured with a setup suitable for the MUNIN cluster.

Example: nextflow run nf-core/rnavar -profile munin

rnavar specific configurations for MUNIN

Specific configurations for MUNIN has been made for rnavar.

Genome references

  • Path to fasta: /data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa
  • Path to fasta_fai: /data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai
  • Path to gtf: /data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf
  • Path to gene_bed: /data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed

Known genome resources

  • Path to dbsnp: /data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz
  • Path to dbsnp_tbi: /data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi
  • Path to known_indels: /data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  • Path to known_indels_tbi: /data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi

STAR index

  • Path to star_index: /data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/STAR.2.7.9a_2x151bp/
  • Params read_length set to 151

Variant annotation configurations

  • Params annotation_cache and cadd_cache set to true
  • Params snpeff_db set to GRCh38.99
  • Params vep_cache_version set to 99
  • Params vep_genome set to GRCh38
  • 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