name: lima description: lima - The PacBio Barcode Demultiplexer and Primer Remover keywords: - sort tools: - lima: description: lima - The PacBio Barcode Demultiplexer and Primer Remover homepage: https://github.com/PacificBiosciences/pbbioconda documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ doi: "" licence: ['BSD-3-Clause-Clear'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - ccs: type: file description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" - primers: type: file description: Fasta file, sequences of primers pattern: "*.fasta" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - bam: type: file description: A bam file of ccs purged of primers pattern: "*.bam" - pbi: type: file description: Pacbio index file of ccs purged of primers pattern: "*.bam" - xml: type: file description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads. pattern: "*.xml" - json: type: file description: A metadata json file pattern: "*.json" - clips: type: file description: A fasta file of clipped primers pattern: "*.clips" - counts: type: file description: A tabulated file of describing pairs of primers pattern: "*.counts" - guess: type: file description: A second tabulated file of describing pairs of primers (no doc available) pattern: "*.guess" - report: type: file description: A tab-separated file about each ZMW, unfiltered pattern: "*.report" - summary: type: file description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered. pattern: "*.summary" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@sguizard"