Determines the depth in a BAM/CRAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
meta2
Groovy Map containing information for the fasta e.g. [ id:‘test’, single_end
meta3
Groovy Map containing information for the fasta_fai e.g. [ id:‘test’, single_end
input
BAM/CRAM file
*.{bam,cram}
input_index
Index of the BAM/CRAM file
*.{bai,crai}
fasta
Reference genome FASTA
*.{fasta,fna,fa}
fasta_fai
Index of the reference genome FASTA
*.fai
versions
File containing software versions
versions.yml
depth
A JSON file containing depth, depth variance, read length and other parameters
*.json
binned_depth
A TSV file containing the binned normalized depth. Can only be calculated for CRAM files
*.tsv
Graph realignment tools for structural variants
