2021-12-14 02:52:37 +00:00
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// rnavar/munin specific profile config
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Praveen Raj (@praveenraj2018)'
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config_profile_description = 'nf-core/rnavar MUNIN profile provided by nf-core/configs'
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config_profile_url = 'https://ki.se/forskning/barntumorbanken'
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// Specific nf-core/rnavar params
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2021-12-14 02:58:54 +00:00
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igenomes_ignore = true
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2021-12-14 02:52:37 +00:00
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// Genome references
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2022-01-20 21:25:31 +00:00
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genome = 'GRCh38'
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2021-12-14 15:10:31 +00:00
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fasta = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa'
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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'
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gtf = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf'
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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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2021-12-14 02:52:37 +00:00
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// Known genome resources
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2021-12-14 15:10:31 +00:00
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dbsnp = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz'
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dbsnp_tbi = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi'
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known_indels = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
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known_indels_tbi = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi'
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2021-12-14 02:52:37 +00:00
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// STAR index
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2021-12-14 20:15:12 +00:00
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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/'
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read_length = 151
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2021-12-14 02:52:37 +00:00
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// Annotation settings
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2021-12-14 15:10:31 +00:00
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annotation_cache = true
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cadd_cache = true
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cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
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cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
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cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
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cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
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snpeff_cache = '/data1/cache/snpEff/'
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snpeff_db = 'GRCh38.99'
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vep_cache = '/data1/cache/VEP/'
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vep_genome = 'GRCh38'
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vep_species = 'homo_sapiens'
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vep_cache_version = '99'
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2021-12-14 02:52:37 +00:00
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}
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