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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
62 lines
1.8 KiB
YAML
62 lines
1.8 KiB
YAML
name: isoseq3_refine
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description: Generate transcripts by clustering HiFi reads
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keywords:
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- isoseq3
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- isoseq3/refine
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tools:
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- isoseq3:
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description: IsoSeq3 - Scalable De Novo Isoform Discovery
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homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
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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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- bam:
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type: file
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description: BAM file, cleaned ccs generated by lima
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pattern: "*.bam"
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- primers:
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type: file
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description: fasta file 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: Set of complete reads (with polyA tail), where the polyA has been trimmed
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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 from polyA trimmed reads
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pattern: "*.pbi"
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- consensusreadset:
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type: file
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description: Metadata about read library
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pattern: "*.xml"
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- summary:
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type: file
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description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads
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pattern: "*.json"
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- report:
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type: file
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description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)
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pattern: "*.csv"
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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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