lima - The PacBio Barcode Demultiplexer and Primer Remover
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
ccs
:file
A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs
*.{bam,fasta,fasta.gz,fastq,fastq.gz}
primers
Fasta file, sequences of primers
*.fasta
counts
*.counts
A tabulated file of describing pairs of primers
report
*.report
A tab-separated file about each ZMW, unfiltered
summary
*.summary
This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
versions_lima
${task.process}
:string
The process the versions were collected from
lima
The tool name
lima --version | head -n1 | sed 's/lima //g' | sed 's/ (.\+//g'
The command used to generate the version of the tool
bam
*.bam
A bam file of ccs purged of primers
pbi
*.bam.pbi
Pacbio index file of ccs purged of primers
fasta
*.{fa,fasta}
A fasta file of ccs purged of primers.
*.fa
fastagz
*.{fa.gz,fasta.gz}
A fasta.gz file of ccs purged of primers.
*.fasta.gz
fastq
*.fastq
A fastq file of ccs purged of primers.
fastqgz
*.fastq.gz
A fastq.gz file of ccs purged of primers.
xml
*.xml
An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.
json
*.json
A metadata json file
clips
*.clips
A fasta file of clipped primers
guess
*.guess
A second tabulated file of describing pairs of primers (no doc available)
versions
