Nextflow Registry | nf-core/ltrretriever/lai@0.0.0-0c7146d

nf-core/ltrretriever/lai @ 0.0.0-0c7146d

Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @GallVp

Maintainers: @GallVp

Estimates the mean LTR sequence identity in the genome. The input genome fasta should have short alphanumeric IDs without comments

Add the following snippet to your workflow script to include this module.

include { LTRRETRIEVER_LAI } from 'nf-core/ltrretriever/lai'

MIT License

Process

`Name`	`LTRRETRIEVER_LAI`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`fasta` file	The genome file that is used to generate everything `*.{fsa,fa,fasta}`

`pass_list` file	A list of intact LTR-RTs generated by LTR_retriever `*.pass.list`

`annotation_out` file	RepeatMasker annotation of all LTR sequences in the genome `*.out`

`monoploid_seqs` file	This parameter is mainly for ployploid genomes. User provides a list of sequence names that represent a monoploid (1x). LAI will be calculated only on these sequences if provided. `*.txt`

Output 3 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.LAI.log` file	Log from LAI `*.LAI.log`

#2 lai_out tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.LAI.out` file	Output file from LAI if LAI is able to estimate the index from the inputs `*.LAI.out`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
lai	Assessing genome assembly quality using the LTR Assembly Index (LAI)	https://github.com/oushujun/LTR_retriever

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:52:45 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fltrretriever%2Flai/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/ltrretriever/lai/blobs/sha256:b9fd8212bb66f02a18d8a9f9432755c9a82d161ab12000c6056892713d8e744a
Size	3.4 KB
Checksum	sha256:b9fd8212bb66f02a18d8a9f9432755c9a82d161ab12000c6056892713d8e744a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:52:45 (UTC)		1	3.4 KB	-