4.40. isnvs_merge_to_vcf¶

4.40.1. Inputs¶

isnvs_merge_to_vcf.assemblies_fasta
Array[File]+ — Default: None
???

isnvs_merge_to_vcf.isnvs_vcf.vphaser2Calls
Array[File] — Default: None
vphaser output; ex. vphaser2..txt.gz

isnvs_merge_to_vcf.reference_fasta
File — Default: None
???

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isnvs_merge_to_vcf.isnvs_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???

isnvs_merge_to_vcf.isnvs_vcf.emailAddress
String? — Default: None
email address passed to NCBI if we need to download reference sequences

isnvs_merge_to_vcf.isnvs_vcf.machine_mem_gb
Int? — Default: None
???

isnvs_merge_to_vcf.isnvs_vcf.naiveFilter
Boolean — Default: false
???

isnvs_merge_to_vcf.isnvs_vcf.sampleNames
Array[String]? — Default: None
list of sample names

isnvs_merge_to_vcf.isnvs_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database

isnvs_merge_to_vcf.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???

isnvs_merge_to_vcf.mafft.machine_mem_gb
Int? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_ep
Float? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_gapOpeningPenalty
Float? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_maxIters
Int? — Default: None
???

isnvs_merge_to_vcf.alignments_by_chr
Array[File]
???

isnvs_merge_to_vcf.isnvs_annot_txt
File
???

isnvs_merge_to_vcf.isnvs_annot_vcf
File
???

isnvs_merge_to_vcf.isnvs_annot_vcf_idx
File
???

isnvs_merge_to_vcf.isnvs_plain_vcf
File
???

isnvs_merge_to_vcf.isnvs_plain_vcf_idx
File
???

isnvs_merge_to_vcf.viral_phylo_version
String
???

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