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nf-configs/conf/pipeline/rnavar/munin.config

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// 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
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igenomes_ignore = true
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// 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'
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// 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'
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// STAR index
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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
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// 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'
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}