nf-core/gfastats @ 0.0.0-6c4ed3a
Summary
A single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation.
Get started
Add the following snippet to your workflow script to include this module.
include { GFASTATS } from 'nf-core/gfastats'
License
MIT License
Name
|
GFASTATS |
|---|
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. |
assembly
tuple
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
|
assembly_summary
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.assembly_summary
file
|
Assembly summary statistics file *.assembly_summary
|
versions_gfastats
tuple
${task.process}
string
|
The name of the process |
|---|---|
gfastats
string
|
The name of the tool |
gfastats -v | sed '1!d;s/.*v//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| gfastats | The swiss army knife for genome assembly. | https://github.com/vgl-hub/gfastats |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:21:22 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgfastats/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gfastats/blobs/sha256:10bbfa4c55e2e00d05e731ea46d9305b2547efc6812858be56e7b359b771c894 |