Nextflow Registry | nf-core/ltrretriever/lai@0.0.0-6c4ed3a

nf-core/ltrretriever/lai @ 0.0.0-6c4ed3a

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:28:09 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fltrretriever%2Flai/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ltrretriever/lai/blobs/sha256:588c59960bb8d88e67e5f3c898438031ad39951e11a203396623cc73d68b7d57
Size	3.5 KB
Checksum	sha256:588c59960bb8d88e67e5f3c898438031ad39951e11a203396623cc73d68b7d57
Downloads	3

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