Nextflow Registry | nf-core/ltrretriever/lai@0.0.0-3fc6d40

nf-core/ltrretriever/lai @ 0.0.0-3fc6d40

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

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:19:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fltrretriever%2Flai/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ltrretriever/lai/blobs/sha256:0eecc8c10a0e75011c1ed4821d0e39338afeff4752dc115b1c7c2ac7e21b1f7d
Size	3.5 KB
Checksum	sha256:0eecc8c10a0e75011c1ed4821d0e39338afeff4752dc115b1c7c2ac7e21b1f7d
Downloads	1

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:28:09 (UTC)	3	3.5 KB
0.0.0-3fc6d40	22 Apr 2026 15:19:41 (UTC)	1	3.5 KB
0.0.0-0c7146d	08 Apr 2026 19:14:43 (UTC)	3	3.4 KB