count how many reads map to each feature
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
input
:file
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
index
Contains indexed bam file
*.bai
meta2
.gtf file information e.g. [ id:'test' ]
[ id:'test' ]
gtf
Contains the features in the GTF format
*.gtf
txt
*.txt
File containing feature counts output
.txt
versions_htseq
${task.process}
:string
The name of the process
htseq
The name of the tool
htseq-count --version
:eval
The expression to obtain the version of the tool
versions
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
