Computes the coverage of different regions from the bam file.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM file
*.{bam,cram}
index
Index of BAM/CRAM file
*.{bai,crai,csi}
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta
Reference genome file. Only needed when passing in CRAM instead of BAM. If not using CRAM, please pass an empty file instead.
*.fasta
cov
${prefix}.bed
The coverage of different regions in bed format. Optional.
*.bed
wig
${prefix}.wig
The coverage of different regions in WIG format. Optional.
*.wig
versions_tiddit
${task.process}
:string
The name of the process
tiddit
The name of the tool
tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'
:eval
The expression to obtain the version of the tool
versions
TIDDIT - structural variant calling.
