Nextflow Registry | nf-core/lima@0.0.0-6c4ed3a

nf-core/lima @ 0.0.0-6c4ed3a

lima - The PacBio Barcode Demultiplexer and Primer Remover

isoseq ccs primer pacbio barcode

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @sguizard

Maintainers: @sguizard

lima - The PacBio Barcode Demultiplexer and Primer Remover

Add the following snippet to your workflow script to include this module.

include { LIMA } from 'nf-core/lima'

MIT License

Process

`Name`	`LIMA`

Input 2 channels

#1 tuple

`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` file	Fasta file, sequences of primers `*.fasta`

Output 14 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bam` file	A bam file of ccs purged of primers `*.bam`

#2 pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.bam.pbi` file	Pacbio index file of ccs purged of primers `*.bam`

#3 xml tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.xml` file	An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads. `*.xml`

#4 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.json` file	A metadata json file `*.json`

#5 clips tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.clips` file	A fasta file of clipped primers `*.clips`

#6 fasta tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.{fa,fasta}` file	A fasta file of ccs purged of primers. `*.fa`

#7 fastq tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.fastq` file	A fastq file of ccs purged of primers. `*.fastq`

#8 guess tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.guess` file	A second tabulated file of describing pairs of primers (no doc available) `*.guess`

#9 counts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.counts` file	A tabulated file of describing pairs of primers `*.counts`

#10 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.report` file	A tab-separated file about each ZMW, unfiltered `*.report`

#11 fastagz tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.{fa.gz,fasta.gz}` file	A fasta.gz file of ccs purged of primers. `*.fasta.gz`

#12 fastqgz