a pangenome-scale aligner
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta_gz{:bash}
:file
BGZIPPED FASTA target file to create the mappings from.
{fa.gz,fna.gz,fasta.gz}
paf{:bash}
Optional inpute file in PAF format to derive the precise alignments for.
*.{paf}
gzi{:bash}
The GZI index of the input FASTA file.
*.{gzi}
fai{:bash}
The FASTA index of the input FASTA file.
*.{fai}
query_self{:bash}
:boolean
If set to true, the input FASTA will also be used as the query FASTA.
fasta_query_list{:bash}
Optional inpute file in FASTA format specifying the query sequences as a list.
*.{fa,fna,fasta}
*.paf{:bash}
Alignments in PAF format
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
