modules/gfastats

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

gfastatsfastagenome assemblygenome summarygenome manipulationgenome statistics

https://github.com/nf-core/modules/[...]/modules/nf-core/gfastats

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:map`

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

`assembly:file`

Draft assembly file

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

`out_fmt:string`

Output format (fasta, fastq, gfa)

`genome_size:integer`

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

`target:string`

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

`meta2:map`

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

`agpfile:file`

converts input agp to path and replaces existing paths.

`meta3:map`

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

`include_bed:file`

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

`meta4:map`

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

`exclude_bed:file`

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

`meta5:map`

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

`instructions:file`

set of instructions provided as an ordered list.

Output

name:type

description

pattern

`assembly_summary`

`meta:map`

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

`*.assembly_summary:file`

Assembly summary statistics file

*.assembly_summary

`assembly`

`meta:map`

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

`*.${out_fmt}.gz:file`

The assembly as modified by gfastats

*.{fasta,fastq,gfa}.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

gfastats
MIT

The swiss army knife for genome assembly.

github.com/vgl-hub/gfastats github.com/vgl-hub/gfastats/tree/main/instructions https://github.com/vgl-hub/gfastats 10.1093/bioinformatics/btac460

modules/gfastats

Description

Input

meta:map

assembly:file

out_fmt:string

genome_size:integer

target:string

meta2:map

agpfile:file

meta3:map

include_bed:file

meta4:map

exclude_bed:file

meta5:map

instructions:file

Output

assembly_summary

meta:map

*.assembly_summary:file

assembly

meta:map

*.${out_fmt}.gz:file

versions

versions.yml:file

Tools

gfastats MIT

`meta:map`

`assembly:file`

`out_fmt:string`

`genome_size:integer`

`target:string`

`meta2:map`

`agpfile:file`

`meta3:map`

`include_bed:file`

`meta4:map`

`exclude_bed:file`

`meta5:map`

`instructions:file`

`assembly_summary`

`meta:map`

`*.assembly_summary:file`

`assembly`

`meta:map`

`*.${out_fmt}.gz:file`

`versions`

`versions.yml:file`

gfastats
MIT