4.45. mafft_and_snp_annotated

Align assemblies with mafft and find SNPs with snp-sites.

4.45.1. Inputs

4.45.1.1. Required inputs

mafft_and_snp_annotated.assembly_fastas
Array[File] — Default: None
Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.

mafft_and_snp_annotated.min_unambig_genome
Int — Default: None
Minimum number of called bases in genome to pass prefilter.

mafft_and_snp_annotated.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar. Uncompressed.

4.45.1.2. Other inputs

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

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

mafft_and_snp_annotated.annotate_vcf.machine_mem_gb
Int? — Default: None
???

mafft_and_snp_annotated.annotate_vcf.output_basename
String — Default: basename(basename(in_vcf,".gz"),".vcf")
???

mafft_and_snp_annotated.annotate_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database. If this is not provided, the ID from the reference fasta will be used (it must be a GenBank accession)

mafft_and_snp_annotated.draft_augur_tree.cpus
Int — Default: 64
???

mafft_and_snp_annotated.draft_augur_tree.disk_size
Int — Default: 1250
???

mafft_and_snp_annotated.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

mafft_and_snp_annotated.draft_augur_tree.exclude_sites
File? — Default: None
???

mafft_and_snp_annotated.draft_augur_tree.machine_mem_gb
Int — Default: 32
???

mafft_and_snp_annotated.draft_augur_tree.method
String — Default: "iqtree"
???

mafft_and_snp_annotated.draft_augur_tree.substitution_model
String — Default: "GTR"
???

mafft_and_snp_annotated.draft_augur_tree.tree_builder_args
String? — Default: None
???

mafft_and_snp_annotated.draft_augur_tree.vcf_reference
File? — Default: None
???

mafft_and_snp_annotated.filter_sequences_by_length.disk_size
Int — Default: 750
???

mafft_and_snp_annotated.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

mafft_and_snp_annotated.mafft.cpus
Int — Default: 64
???

mafft_and_snp_annotated.mafft.disk_size
Int — Default: 750
???

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

mafft_and_snp_annotated.mafft.keep_length
Boolean — Default: true
???

mafft_and_snp_annotated.mafft.large
Boolean — Default: false
???

mafft_and_snp_annotated.mafft.mem_size
Int — Default: 500
???

mafft_and_snp_annotated.mafft.memsavetree
Boolean — Default: false
???

mafft_and_snp_annotated.mafft.remove_reference
Boolean — Default: false
???

mafft_and_snp_annotated.run_iqtree
Boolean — Default: false
???

mafft_and_snp_annotated.snp_sites.allow_wildcard_bases
Boolean — Default: true
???

mafft_and_snp_annotated.snp_sites.disk_size
Int — Default: 750
???

mafft_and_snp_annotated.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???

mafft_and_snp_annotated.zcat.cpus
Int — Default: 4
???

4.45.2. Outputs

mafft_and_snp_annotated.combined_assemblies
File
???

mafft_and_snp_annotated.ml_tree
File?
???

mafft_and_snp_annotated.multiple_alignment
File
???

mafft_and_snp_annotated.unmasked_snps
File
???

mafft_and_snp_annotated.unmasked_snps_annotated
File
???

mafft_and_snp_annotated.unmasked_snps_annotated_tbi
File
???

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