Generates a count of coverage of alleles
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_index
BAM/CRAM/SAM index file
*.{bai,crai,sai}
loci
loci file
*.{tsv}
fasta
Input genome fasta file. Required when passing CRAM files.
allelecount
*.alleleCount
Allele count file
*.{alleleCount}
versions_allelecounter
${task.process}
:string
The name of the process
alleleCounter
The name of the tool
alleleCounter --version
:eval
The expression to obtain the version of the tool
versions
Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)
