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