mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-23 18:58:16 +00:00
44 lines
2.3 KiB
Text
44 lines
2.3 KiB
Text
// rnavar/munin specific profile config
|
|
|
|
params {
|
|
// Specific nf-core/configs params
|
|
config_profile_contact = 'Praveen Raj (@praveenraj2018)'
|
|
config_profile_description = 'nf-core/rnavar MUNIN profile provided by nf-core/configs'
|
|
config_profile_url = 'https://ki.se/forskning/barntumorbanken'
|
|
|
|
// Specific nf-core/rnavar params
|
|
|
|
igenomes_ignore = true
|
|
|
|
// Genome references
|
|
genome = 'GRCh38'
|
|
fasta = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa'
|
|
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'
|
|
gtf = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf'
|
|
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
|
|
dbsnp = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz'
|
|
dbsnp_tbi = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi'
|
|
known_indels = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
|
|
known_indels_tbi = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi'
|
|
|
|
// STAR index
|
|
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/'
|
|
read_length = 151
|
|
|
|
// Annotation settings
|
|
annotation_cache = true
|
|
cadd_cache = true
|
|
cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
|
|
cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
|
|
cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
|
|
cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
|
|
snpeff_cache = '/data1/cache/snpEff/'
|
|
snpeff_db = 'GRCh38.99'
|
|
vep_cache = '/data1/cache/VEP/'
|
|
vep_genome = 'GRCh38'
|
|
vep_species = 'homo_sapiens'
|
|
vep_cache_version = '99'
|
|
|
|
}
|