TranscriptClean-NF/modules/local/transcriptclean/meta.yml at main · borgessbarbara/TranscriptClean-NF · GitHub

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---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: transcriptclean
## TODO nf-core: Add a description of the module and list keywords
description: Nextflow module of TranscriptClean
keywords:
  - bioinformatics
  - long-reads
  - alignment
  - correction
  - mismatches
  - indels
  - splice-junctions
tools:
  - transcriptclean:
      description: |
        Correct mismatches, microindels, and noncanonical splice junctions
        in long reads that have been mapped to the genome
      homepage: https://github.com/mortazavilab/TranscriptClean
      documentation: https://github.com/mortazavilab/TranscriptClean/wiki
      tool_dev_url: https://github.com/mortazavilab/TranscriptClean
      doi: 10.1093/bioinformatics/bty483
      licence: ["MIT"]
      identifier: ""

## TODO nf-core: Add a description of all of the variables used as input
input:
  # Only when we have meta
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'sample1' ]

    ## TODO nf-core: Delete / customise this example input
    - sam:
        type: file
        description: Sorted SAM file
        pattern: "*.{sam}"
        ontologies:
          - edam: "http://edamontology.org/format_3462" # SAM
    - fasta:
        type: file
        description: Genome FASTA file
        pattern: "*.{fasta,fa}"
        ontologies:
          - edam: "http://edamontology.org/format_1929" # FASTA
    - vcf:
        type: file
        description: (Optional) VCF file of variants for variant-aware correction.
        pattern: "*.{vcf}"
        ontologies:
          - edam: "http://edamontology.org/format_3016" # VCF
    - splice_junctions:
        type: file
        description: (Optional) Splice junction file for noncanonical splice junction correction.
        pattern: "*.{tab,txt}"
    - gtf:
        type: file
        description: (Optional) GTF file for generating splice junction file.
        pattern: "*.{vcf}"
    - transcriptclean_logs:
        type: file
        description: Output files from TranscriptClean for report
        pattern: "*.{clean.TE.log, clean.log}"

## TODO nf-core: Add a description of all of the variables used as output
output:
  - results:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1' ]`
      ## TODO nf-core: Delete / customise this example output
      - transcriptclean_sam:
          type: file
          description: Corrected SAM file
          pattern: "*.{sam}"
          ontologies:
            - edam: "http://edamontology.org/format_3462" # SAM
      - splice_junctions_extracted:
          type: file
          description: Splice junctions extracted from GTF file
          pattern: "*.{txt}"
      - corrected_fasta:
          type: file
          description: corrected FASTA file of transcripts
          pattern: "*.{fasta,fa}"
          ontologies:
            - edam: "http://edamontology.org/format_1929" # FASTA
      - TE_error_log:
          type: file
          description: Transcript error log file
          pattern: "*.{clean.TE.log}"
      - TE_log:
          type: file
          description: Transcript log file
          pattern: "*.{clean.log}"
      - report:
          type: file
          description: PDF TranscriptClean Report from logs
          pattern: "*.{_report.pdf}"
  - versions:
      - "versions.yml":
          type: file
          description: File containing software versions
          pattern: "versions.yml"

authors:
  - "@borgessbarbara"
maintainers:
  - "@borgessbarbara"