Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.
meta
:map
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
bam
:file
Name-Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2
Groovy Map containing annotation information e.g. [ id:'genome' ]
[ id:'genome' ]
index
:directory
Annotation index created by mudskipper/index
gtf
Annotation file
*.{gtf,gff,gff3}
rad
:string
File type
${prefix}.bam
Sorted BAM file
*.bam
${prefix}.rad
RAD file
*.rad
versions_mudskipper
${task.process}
The name of the process
mudskipper
The name of the tool
mudskipper -V 2>&1 | sed 's/.*mudskipper //'
:eval
The expression to obtain the version of the tool
versions
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
