Computes the coverage of different regions from the bam file.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM file
*.{bam,cram}
index{:bash}
Index of BAM/CRAM file
*.{bai,crai,csi}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta{:bash}
Reference genome file. Only needed when passing in CRAM instead of BAM. If not using CRAM, please pass an empty file instead.
*.fasta
cov{:bash}
*.bed{:bash}
The coverage of different regions in bed format. Optional.
*.bed
wig{:bash}
*.wig{:bash}
The coverage of different regions in WIG format. Optional.
*.wig
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
TIDDIT - structural variant calling.
