Description

a pangenome-scale aligner

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta_gz (file)

BGZIPPED FASTA target file to create the mappings from.

{fa.gz,fna.gz,fasta.gz}

paf (file)

Optional inpute file in PAF format to derive the precise alignments for.

*.{paf}

query_self (boolean)

If set to true, the input FASTA will also be used as the query FASTA.

gzi (file)

The GZI index of the input FASTA file.

*.{gzi}

fai (file)

The FASTA index of the input FASTA file.

*.{fai}

fasta_query_list (file)

Optional inpute file in FASTA format specifying the query sequences as a list.

*.{fa,fna,fasta}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

paf (file)

Alignments in PAF format

*.{paf}

versions (file)

File containing software versions

versions.yml

Tools

wfmash
MIT

a pangenome-scale aligner