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}
${prefix}.bed{:bash}
The coverage of different regions in bed format. Optional.
*.bed
wig{:bash}
${prefix}.wig{:bash}
The coverage of different regions in WIG format. Optional.
*.wig
versions_tiddit{:bash}
${task.process}{:bash}
:string
The name of the process
tiddit{:bash}
The name of the tool
tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
TIDDIT - structural variant calling.
