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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>
60 lines
2.5 KiB
YAML
60 lines
2.5 KiB
YAML
name: gstama_merge
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description: Merge multiple transcriptomes while maintaining source information.
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keywords:
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- gstama
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- gstama/merge
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- long-read
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- isoseq
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- nanopore
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- tama
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- trancriptome
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- annotation
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tools:
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- gstama:
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description: Gene-Switch Transcriptome Annotation by Modular Algorithms
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homepage: https://github.com/sguizard/gs-tama
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documentation: https://github.com/GenomeRIK/tama/wiki
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tool_dev_url: https://github.com/sguizard/gs-tama
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doi: "https://doi.org/10.1186/s12864-020-07123-7"
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licence: ["GPL v3 License"]
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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', single_end:false ]
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- bed:
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type: file
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description: bed12 file generated by TAMA collapse
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pattern: "*.bed"
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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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- bed:
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type: file
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description: This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta.
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pattern: "*.bed"
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- gene_report:
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type: file
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description: This contains a report of the genes from the merged file. "num_clusters" refers to the number of source transcripts that were used to make this gene model. "num_final_trans" refers to the number of transcripts in the final gene model.
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pattern: "*_gene_report.txt"
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- merge:
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type: file
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description: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the "txt" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix.
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pattern: "*_merge.txt"
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- trans_report:
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type: file
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description: This contains the source information for each merged transcript.
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pattern: "*_trans_report.txt"
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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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