4.26. isnvs_merge_to_vcf¶
4.26.1. Inputs¶
4.26.1.1. Required 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.
isnvs_merge_to_vcf.reference_fasta
File — Default: None
???
4.26.1.2. Other inputs¶
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isnvs_merge_to_vcf.isnvs_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???
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"
???
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
???
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