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