Calls consensus sequences from reads with the same unique molecular tag.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, collapse:false ]
grouped_bam{:bash}
:file
The input SAM or BAM file, grouped by UMIs
*.{bam,sam}
min_reads{:bash}
:integer
Minimum number of original reads to build each consensus read.
min_baseq{:bash}
Ignore bases in raw reads that have Q below this value.
bam{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.bam{:bash}
Output SAM or BAM file to write consensus reads.
versions_fgbio{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
fgbio{:bash}
The tool name
fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Tools for working with genomic and high throughput sequencing data.
