Estimates the numbers of unique molecules in a sequencing library.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta{:bash}
The reference fasta file
*.fasta
fai{:bash}
Index of reference fasta file
fasta.fai
dict{:bash}
GATK sequence dictionary
*.dict
metrics{:bash}
*.metrics{:bash}
File containing metrics on the input files
*.{metrics}
versions_gatk4{:bash}
${task.process}{:bash}
:string
The name of the process
gatk4{:bash}
The name of the tool
gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Genome Analysis Toolkit (GATK4)
