Computes equivalence classes for reads and quantifies abundances
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
*.{fastq,fastq.gz}
meta2{:bash}
index{:bash}
Kallisto genome index.
*.idx
gtf{:bash}
Optional gtf file for translation of transcripts into genomic coordinates.
*.gtf
chromosomes{:bash}
Optional tab separated file with chromosome names and lengths.
*.tsv
fragment_length{:bash}
:integer
For single-end mode only, the estimated average fragment length.
fragment_length_sd{:bash}
For single-end mode only, the estimated standard deviation of the fragment length.
results{:bash}
${prefix}{:bash}
Kallisto output file
json_info{:bash}
*.run_info.json{:bash}
JSON file containing information about the run
*.run_info.json
log{:bash}
*.log{:bash}
File containing log information from running kallisto quant
*.log.txt
versions_kallisto{:bash}
${task.process}{:bash}
:string
The name of the process
kallisto{:bash}
The name of the tool
kallisto version | sed 's/.*version //'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
