Purge haplotigs and overlaps for an assembly
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
basecov{:bash}
:file
A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT
*.PB.base.cov
cutoff{:bash}
A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS
*.cutoffs
paf{:bash}
A file of assembly alignments to itself
*.paf(.gz)?
bed{:bash}
*.dups.bed.gz{:bash}
A bed file of sequences purged of false duplications
*.bed.gz
log{:bash}
*.purge_dups.log{:bash}
A log of the tool output
*.log
versions_purgedups{:bash}
${task.process}{:bash}
:string
The name of the process
purge_dups{:bash}
The name of the tool
1.2.6{:bash}
The expression to obtain the version of the tool
versions{:bash}
Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
