Determines the depth in a BAM/CRAM file
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM file
*.{bam,cram}
input_index
Index of the BAM/CRAM file
*.{bai,crai}
meta2
Groovy Map containing information for the fasta e.g. [ id:‘test’, single_end:false ]
fasta
Reference genome FASTA
*.{fasta,fna,fa}
meta3
Groovy Map containing information for the fasta_fai e.g. [ id:‘test’, single_end:false ]
fasta_fai
Index of the reference genome FASTA
*.fai
depth
*.json
A JSON file containing depth, depth variance, read length and other parameters
binned_depth
*.tsv
A TSV file containing the binned normalized depth. Can only be calculated for CRAM files
versions_paragraph
${task.process}
:string
The name of the process
paragraph
The name of the tool
2.3
The expression to obtain the version of the tool
versions
Graph realignment tools for structural variants
