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