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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>
76 lines
2 KiB
YAML
76 lines
2 KiB
YAML
name: plasmidid
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description: assembles bacterial plasmids
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keywords:
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- assembly
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- plasmid
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- bacterial
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tools:
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- plasmidid:
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description: Pipeline for plasmid identification and reconstruction
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homepage: https://github.com/BU-ISCIII/plasmidID/wiki
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documentation: https://github.com/BU-ISCIII/plasmidID#readme
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tool_dev_url: https://github.com/BU-ISCIII/plasmidID
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doi: ""
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licence: ["GPL v3"]
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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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- scaffold:
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type: file
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description: |
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Fasta file containing scaffold
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- fasta:
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type: file
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description: FASTA reference file
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pattern: "*.{fasta,fa}"
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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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- html:
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type: file
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description: html file with results rendered
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pattern: "*.{html}"
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- tab:
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type: file
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description: Results in a tabular file
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pattern: "*.{tab}"
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- images:
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type: directory
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description: Directory containing the images produced by plasmidid
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pattern: "images"
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- logs:
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type: directory
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description: Directory containing the logs produced by plasmidid
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pattern: "logs"
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- data:
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type: directory
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description: Directory containing the data produced by plasmidid
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pattern: "data"
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- database:
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type: directory
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description: Directory containing the database produced by plasmidid
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pattern: "database"
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- fasta_files:
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type: directory
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description: Directory containing the fasta files produced by plasmidid
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pattern: "fasta_files"
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- kmer:
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type: directory
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description: Directory containing the kmer files produced by plasmidid
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pattern: "database"
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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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- "@joseespinosa"
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- "@drpatelh"
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