Description

A single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Input

name:type
description
pattern

meta{:bash}

:map

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

assembly{:bash}

:file

Draft assembly file

*.{fasta,fastq,gfa}(.gz)?

out_fmt{:bash}

:string

Output format (fasta, fastq, gfa)

genome_size{:bash}

:integer

estimated genome size (bp) for NG* statistics (optional).

target{:bash}

:string

target specific sequence by header, optionally with coordinates (optional).

meta2{:bash}

:map

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

agpfile{:bash}

:file

converts input agp to path and replaces existing paths.

meta3{:bash}

:map

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

include_bed{:bash}

:file

generates output on a subset list of headers or coordinates in 0-based bed format.

meta4{:bash}

:map

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

exclude_bed{:bash}

:file

opposite of —include-bed. They can be combined (no coordinates).

meta5{:bash}

:map

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

instructions{:bash}

:file

set of instructions provided as an ordered list.

Output

name:type
description
pattern

assembly_summary{:bash}

meta{:bash}

:map

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

*.assembly_summary{:bash}

:file

Assembly summary statistics file

*.assembly_summary

assembly{:bash}

meta{:bash}

:map

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

*.${out_fmt}.gz{:bash}

:file

The assembly as modified by gfastats

*.{fasta,fastq,gfa}.gz

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mahesh-panchal
get in touch
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