Nextflow Registry | nf-core/simpleaf/index@0.0.0-6c4ed3a

nf-core/simpleaf/index @ 0.0.0-6c4ed3a

Indexing of transcriptome for gene expression quantification using SimpleAF

indexing transcriptome gene expression SimpleAF

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords @dongzehe

Maintainers: @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords @dongzehe

Indexing of transcriptome for gene expression quantification using SimpleAF

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

include { SIMPLEAF_INDEX } from 'nf-core/simpleaf/index'

MIT License

Process

`Name`	`SIMPLEAF_INDEX`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing information on genome_fasta and genome_gtf
`genome_fasta` file	FASTA file containing the genome sequence. It must be provided together with the corresponding genome_gtf file. When another input set is provided, it must be empty (provided as []).
`genome_gtf` file	GTF file containing gene annotations. It must be provided together with its corresponding genome_fasta file. When another input set rather than genome_fasta + genome_gtf is provided, it must be empty (provided as []).

#2 tuple

`meta2` map	Groovy Map containing information on transcript_fasta
`transcript_fasta` file	FASTA file containing the transcript sequences to build index directly on. When another input set is provided, it must be empty (provided as []).

#3 tuple

`meta3` map	Groovy Map containing information on probe_csv.
`probe_csv` file	CSV file containing the reference probe sequences to build index directly on. When another input set is provided, it must be empty (provided as []).

#4 tuple

`meta4` map	Groovy Map containing information on feature_csv.
`feature_csv` file	CSV file containing the reference feature barcodes to build index directly on. When another input set is provided, it must be empty (provided as []).

Output 4 channels

#1 ref tuple

`meta` map	Groovy Map containing information on the index generated by simpleaf
`${prefix}/ref` map	Groovy Map containing information on the transcriptomic reference constructed by simpleaf.

#2 t2g tuple

`meta` map	Groovy Map containing information on the index generated by simpleaf
`${prefix}/ref/{t2g,t2g_3col}.tsv` file	Path to the tsv file containing the transcript-to-gene mapping information generated by simpleaf. This is used as --t2g-map when invoking simpleaf quant.

#3 index tuple

`meta` map	Groovy Map containing information on the index generated by simpleaf
`${prefix}/index` map	Groovy Map containing information on the index generated by simpleaf

#4 versions

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

Tool	Description	Homepage
simpleaf	SimpleAF is a tool for quantification of gene expression from RNA-seq data	https://github.com/COMBINE-lab/simpleaf

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:46:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsimpleaf%2Findex/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/simpleaf/index/blobs/sha256:615b123e7f720a4319cee16e38be167f17da548f3abde8307709206c77725e40
Size	4.1 KB
Checksum	sha256:615b123e7f720a4319cee16e38be167f17da548f3abde8307709206c77725e40