millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-21 16:16:04 +00:00
Code Issues Releases Packages Activity

Addressed review feedback

Browse source
This commit is contained in:
Praveen 2021-12-14 03:58:54 +01:00
parent b4d5330c0e
commit cc1fe5b5a0
1 changed files with 22 additions and 22 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

44
conf/pipeline/rnavar/munin.config
View file

@ -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'
}