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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>
59 lines
1.9 KiB
YAML
59 lines
1.9 KiB
YAML
name: transdecoder_predict
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description: TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf
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keywords:
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- eukaryotes
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- gff
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tools:
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- transdecoder:
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description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
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homepage: https://github.com/TransDecoder
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documentation: https://github.com/TransDecoder/TransDecoder/wiki
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tool_dev_url: https://github.com/TransDecoder/TransDecoder
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doi: ""
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licence: ["Broad Institute"]
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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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- fasta:
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type: file
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description: fasta file
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pattern: "*.{fasta}"
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- fold:
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type: folder
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description: Output from the module transdecoder_longorf
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pattern: "*"
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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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- 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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- pep:
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type: amino acids fasta file
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description: All ORFs meeting the minimum length criteria, regardless of coding potential
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pattern: "*.{pep}"
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- gff3:
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type: gff3 file
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description: Positions of all ORFs as found in the target transcripts
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pattern: "*.{gff3}"
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- cds:
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type: nucleotide fasta file
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description: the nucleotide coding sequence for all detected ORFs
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pattern: "*{cds}"
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- bed:
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type: bed file
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description: bed file
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pattern: "*{bed}"
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authors:
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- "@Danilo2771"
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