Description

Indexing of transcriptome for gene expression quantification using SimpleAF

Input

name:type
description
pattern

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 []).

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 []).

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 []).

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

name:type
description
pattern

index

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

ref

meta:map

Groovy Map containing information on the transcriptomic reference constructed by simpleaf.

${prefix}/ref:map

Groovy Map containing information on the transcriptomic reference constructed by simpleaf.

t2g

meta: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.

${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.

versions

versions.yml:file

File containing software versions

versions.yml

Tools

simpleaf
BSD-3-Clause

SimpleAF is a tool for quantification of gene expression from RNA-seq data