munin.config

// 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'
}