Description

Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.

Input

Name (Type)
Description
Pattern

meta (map)

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

bam (file)

Name-Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

gtf (file)

Annotation file

*.{gtf,gff,gff3}

index (directory)

Annotation index created by mudskipper/index

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

bam (file)

Sorted BAM file

*.bam

rad (file)

RAD file

*.rad

Tools

mudskipper
BSD 3-clause

mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.