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3aacd46da2
* backfilled modules with meta.yml that had no license identifier * harmonized BSD license names * whitespace linting at modules/unzip/meta.yml:12 * harmonized software from US NIH-NCBI/NIST to 'US-Government-Work' * Update modules/bcftools/index/meta.yml `bcftools` is dual-licensed, use associative array to allow for multiple licenses Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Michael L Heuer <heuermh@acm.org>
81 lines
2.6 KiB
YAML
81 lines
2.6 KiB
YAML
name: isoseq3_cluster
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description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
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keywords:
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- cluster
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tools:
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- isoseq3:
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description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
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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 generated by isoseq3 refine
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pattern: "*.bam"
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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', single_end:false ]
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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- bam:
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type: file
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description: BAM file of clustered consensus
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pattern: "*.transcripts.bam"
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- pbi:
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type: file
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description: Pacbio Index of consensus reads generated by clustering
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pattern: "*.transcripts.bam.pbi"
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- cluster:
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type: file
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description: A two columns (from, to) file describing original read name to new read name
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pattern: "*.transcripts.cluster"
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- cluster_report:
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type: file
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description: A table files clusters (transcripts) members (read)
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pattern: "*.transcripts.cluster_report.csv"
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- transcriptset:
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type: file
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description: A metadata xml file which contains full paths to data files
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pattern: "*.transcripts.transcriptset.xml"
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- hq_bam:
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type: file
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description: High quality reads (when --use-qvs is set)
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pattern: "*.transcripts.hq.bam"
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- hq_pbi:
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type: file
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description: Pacbio index of high quality reads (when --use-qvs is set)
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pattern: "*.transcripts.hq.bam.pbi"
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- lq_bam:
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type: file
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description: Low quality reads (when --use-qvs is set)
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pattern: "*.transcripts.lq.bam"
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- lq_pbi:
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type: file
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description: Pacbio index of low quality reads (when --use-qvs is set)
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pattern: "*.transcripts.lq.bam.pbi"
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- singletons_bam:
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type: file
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description: Unclustered reads (when --singletons is set)
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pattern: "*.transcripts.singletons.bam"
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- singletons_pbi:
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type: file
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description: Pacbio index of unclustered reads (when --singletons is set)
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pattern: "*.transcripts.singletons.bam.pbi"
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authors:
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- "@sguizard"
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