Plot whole genome coverage from BAM/CRAM file as SVG
meta:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
bam:file
BAM/CRAM file from alignment
*.{bam,cram}
bai:file
BAI/CRAI file from alignment
*.{bai,crai}
meta2:map
Groovy Map containing reference information e.g. [ id:‘test_reference’ ]
fasta:file
The reference fasta file
*.fasta
meta3:map
Groovy Map containing reference fai information e.g. [ id:‘test_reference’ ]
fai:file
Index of reference fasta file
fasta.fai
meta4:map
Groovy Map containing reference dict information e.g. [ id:‘test_reference’ ]
dict:file
GATK sequence dictionary
*.dict
output
Groovy Map containing Sample information e.g. [ id:‘test’, single_end:false ]
*.svg:file
Output SVG file
*.svg
versions
versions.yml:file
File containing software versions
versions.yml
Java utilities for Bioinformatics.
