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