Nextflow Registry | nf-core/kallisto/quant@0.0.0-6c4ed3a

nf-core/kallisto/quant @ 0.0.0-6c4ed3a

Computes equivalence classes for reads and quantifies abundances

quant kallisto pseudoalignment

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @anoronh4

Maintainers: @anoronh4

Computes equivalence classes for reads and quantifies abundances

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

include { KALLISTO_QUANT } from 'nf-core/kallisto/quant'

MIT License

Process

`Name`	`KALLISTO_QUANT`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. `*.{fastq,fastq.gz}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`index` file	Kallisto genome index. `*.idx`

`gtf` file	Optional gtf file for translation of transcripts into genomic coordinates. `*.gtf`

`chromosomes` file	Optional tab separated file with chromosome names and lengths. `*.tsv`

`fragment_length` integer	For single-end mode only, the estimated average fragment length.

`fragment_length_sd` integer	For single-end mode only, the estimated standard deviation of the fragment length.

Output 4 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	File containing log information from running kallisto quant `*.log.txt`

#2 results tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}` file	Kallisto output file

#3 json_info tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.run_info.json` file	JSON file containing information about the run `*.run_info.json`

#4 versions_kallisto tuple

`${task.process}` string	The name of the process
`kallisto` string	The name of the tool
`kallisto version \| sed 's/.*version //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
kallisto	Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.	https://pachterlab.github.io/kallisto/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:26:43 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fkallisto%2Fquant/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/kallisto/quant/blobs/sha256:9b1c4a55a9bf76a3fc1725b81563fb2967767d25d0a168641cc10671628440e8
Size	3.5 KB
Checksum	sha256:9b1c4a55a9bf76a3fc1725b81563fb2967767d25d0a168641cc10671628440e8
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:26:43 (UTC)		3	3.5 KB