Computes equivalence classes for reads and quantifies abundances
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.
*.{fastq,fastq.gz}
meta2:map
index:file
Kallisto genome index.
*.idx
gtf:file
Optional gtf file for translation of transcripts into genomic coordinates.
*.gtf
chromosomes:file
Optional tab separated file with chromosome names and lengths.
*.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.
results
${prefix}:file
Kallisto output file
json_info
*.run_info.json:file
JSON file containing information about the run
*.run_info.json
log
*.log:file
File containing log information from running kallisto quant
*.log.txt
versions
versions.yml:file
File containing software versions
versions.yml
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
