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