Computes equivalence classes for reads and quantifies abundances
Input
name:type
description
pattern
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. Pass --fr-stranded or --rf-stranded via ext.args to select
strandedness; kallisto is unstranded by default.
*.{fastq,fastq.gz}
meta2
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
index
:file
Kallisto genome index.
*.idx
gtf
:file
Optional gtf file for translation of transcripts into genomic
coordinates. Pass [] to omit.
*.gtf
chromosomes
:file
Optional tab separated file with chromosome names and lengths.
Pass [] to omit.
*.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
name:type
description
pattern
results
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}
:file
Kallisto output file
json_info
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
log
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
versions_kallisto
${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
Topics
name:type
description
pattern
versions
${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
Tools
kallisto
BSD_2_clause
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
