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2.5 KiB
2.5 KiB
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 to151
Variant annotation configurations
- Params
annotation_cache
andcadd_cache
set totrue
- Params
snpeff_db
set toGRCh38.99
- Params
vep_cache_version
set to99
- Params
vep_genome
set toGRCh38
- 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