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* create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder_longorf reviewed main.nf * removed predict * test.yml updated * pytest run Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
57 lines
1.8 KiB
YAML
57 lines
1.8 KiB
YAML
name: transdecoder_longorf
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description: TransDecoder itentifies candidate coding regions within transcript sequences. it is used to build gff file.
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keywords:
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- eucaryotes
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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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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. file
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pattern: "*.{pep}"
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- gff3:
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type: gff file
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description: positions of all ORFs as found in the target transcripts. file
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pattern: "*.{gff3}"
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- cds:
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type: fasta file
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description: the nucleotide coding sequence for all detected ORFs. file
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pattern: "*{cds}"
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- dat:
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type: tsv file
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description: nucleotide frequencies
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pattern: "*{dat}"
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- folder:
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type: folder
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description: contains all the files from the run
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authors:
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- "@Danilo2771"
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