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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>
85 lines
2.4 KiB
YAML
85 lines
2.4 KiB
YAML
name: bakta
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description: Rapid annotation of bacterial genomes & plasmids.
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keywords:
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- annotation
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- fasta
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- prokaryote
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tools:
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- bakta:
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description: Rapid & standardized annotation of bacterial genomes & plasmids.
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homepage: https://github.com/oschwengers/bakta
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documentation: https://github.com/oschwengers/bakta
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tool_dev_url: https://github.com/oschwengers/bakta
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doi: "10.1099/mgen.0.000685"
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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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- fasta:
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type: file
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description: |
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FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
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- db:
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type: file
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description: |
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Path to the Bakta database
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- proteins:
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type: file
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description: FASTA file of trusted proteins to first annotate from (optional)
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- prodigal_tf:
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type: file
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description: Training file to use for Prodigal (optional)
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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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- tsv:
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type: file
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description: annotations as simple human readble tab separated values
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pattern: "*.tsv"
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- gff:
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type: file
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description: annotations & sequences in GFF3 format
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pattern: "*.gff3"
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- gbff:
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type: file
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description: annotations & sequences in (multi) GenBank format
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pattern: "*.gbff"
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- embl:
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type: file
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description: annotations & sequences in (multi) EMBL format
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pattern: "*.embl"
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- fna:
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type: file
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description: replicon/contig DNA sequences as FASTA
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pattern: "*.fna"
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- faa:
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type: file
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description: CDS/sORF amino acid sequences as FASTA
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pattern: "*.faa"
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- ffn:
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type: file
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description: feature nucleotide sequences as FASTA
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pattern: "*.ffn"
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- hypotheticals_tsv:
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type: file
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description: further information on hypothetical protein CDS as simple human readble tab separated values
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pattern: "*.hypotheticals.tsv"
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- hypotheticals_faa:
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type: file
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description: hypothetical protein CDS amino acid sequences as FASTA
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pattern: "*.hypotheticals.faa"
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authors:
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- "@rpetit3"
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