diff --git a/conf/pipeline/rnavar/munin.config b/conf/pipeline/rnavar/munin.config index a970fe8..70e3ac6 100644 --- a/conf/pipeline/rnavar/munin.config +++ b/conf/pipeline/rnavar/munin.config @@ -8,35 +8,35 @@ params { // Specific nf-core/rnavar params - igenomes_ignore = true + igenomes_ignore = true // Genome references - 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' + 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' + 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/star150bp.idx/' + star_index = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/' // 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' + 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' }