mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
77 lines
2.2 KiB
YAML
77 lines
2.2 KiB
YAML
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"
|