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
