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