Description

count how many reads map to each feature

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

input:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

index:file

Contains indexed bam file

*.bai

meta2:map

.gtf file information e.g. [ id:'test' ]

gtf:file

Contains the features in the GTF format

*.gtf

Output

name:type
description
pattern

txt

meta:map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

*.txt:file

File containing feature counts output

.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

htseq/count
GPL v3

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.