modules/simpleaf_index

Indexing of transcriptome for gene expression quantification using SimpleAF

indexingtranscriptomegene expressionSimpleAF

https://github.com/nf-core/modules/[...]/modules/nf-core/simpleaf/index

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 index generated by simpleaf

`${prefix}/ref`
`:map`

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

`t2g`

`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.

`versions_alevin_fry`

`${task.process}`
`:string`

The name of the process

`alevin-fry`
`:string`

The name of the tool

`alevin-fry --version | sed 's/alevin-fry //'`
`:eval`

The expression to obtain the version of the tool

`versions_piscem`

`${task.process}`
`:string`

The name of the process

`piscem`
`:string`

The name of the tool

`piscem --version | sed 's/piscem //'`
`:eval`

The expression to obtain the version of the tool

`versions_simpleaf`

`${task.process}`
`:string`

The name of the process

`simpleaf`
`:string`

The name of the tool

`ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`alevin-fry`
`:string`

The name of the tool

`alevin-fry --version | sed 's/alevin-fry //'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`piscem`
`:string`

The name of the tool

`piscem --version | sed 's/piscem //'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`simpleaf`
`:string`

The name of the tool

`ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'`
`:eval`

The expression to obtain the version of the tool

Tools

simpleaf
BSD-3-Clause

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

github.com/COMBINE-lab/simpleaf

modules/simpleaf_index

Description

Input

meta:map

genome_fasta:file

genome_gtf:file

meta2:map

transcript_fasta:file

meta3:map

probe_csv:file

meta4:map

feature_csv:file

Output

index

meta:map

${prefix}/index:map

ref

meta:map

${prefix}/ref:map

t2g

meta:map

${prefix}/ref/{t2g,t2g_3col}.tsv:file

versions_alevin_fry

${task.process}:string

alevin-fry:string

alevin-fry --version | sed 's/alevin-fry //':eval

versions_piscem

${task.process}:string

piscem:string

piscem --version | sed 's/piscem //':eval

versions_simpleaf

${task.process}:string

simpleaf:string

ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //':eval

Topics

versions

${task.process}:string

alevin-fry:string

alevin-fry --version | sed 's/alevin-fry //':eval

${task.process}:string

piscem:string

piscem --version | sed 's/piscem //':eval

${task.process}:string

simpleaf:string

ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //':eval

Tools

simpleaf BSD-3-Clause

included in

maintainers

get in touch

`meta`
`:map`

`genome_fasta`
`:file`

`genome_gtf`
`:file`

`meta2`
`:map`

`transcript_fasta`
`:file`

`meta3`
`:map`

`probe_csv`
`:file`

`meta4`
`:map`

`feature_csv`
`:file`

`index`

`meta`
`:map`

`${prefix}/index`
`:map`

`ref`

`meta`
`:map`

`${prefix}/ref`
`:map`

`t2g`

`meta`
`:map`

`${prefix}/ref/{t2g,t2g_3col}.tsv`
`:file`

`versions_alevin_fry`

`${task.process}`
`:string`

`alevin-fry`
`:string`

`alevin-fry --version | sed 's/alevin-fry //'`
`:eval`

`versions_piscem`

`${task.process}`
`:string`

`piscem`
`:string`

`piscem --version | sed 's/piscem //'`
`:eval`

`versions_simpleaf`

`${task.process}`
`:string`

`simpleaf`
`:string`

`ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'`
`:eval`

`versions`

`${task.process}`
`:string`

`alevin-fry`
`:string`

`alevin-fry --version | sed 's/alevin-fry //'`
`:eval`

`${task.process}`
`:string`

`piscem`
`:string`

`piscem --version | sed 's/piscem //'`
`:eval`

`${task.process}`
`:string`

`simpleaf`
`:string`

`ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'`
`:eval`

simpleaf
BSD-3-Clause