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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>
91 lines
2.7 KiB
YAML
91 lines
2.7 KiB
YAML
name: prokka
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description: Whole genome annotation of small genomes (bacterial, archeal, viral)
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keywords:
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- annotation
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- fasta
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- prokka
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tools:
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- prokka:
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description: Rapid annotation of prokaryotic genomes
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homepage: https://github.com/tseemann/prokka
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doi: "10.1093/bioinformatics/btu153"
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licence: ["GPL v2"]
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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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- 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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- gff:
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type: file
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description: annotation in GFF3 format, containing both sequences and annotations
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pattern: "*.{gff}"
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- gbk:
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type: file
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description: annotation in GenBank format, containing both sequences and annotations
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pattern: "*.{gbk}"
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- fna:
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type: file
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description: nucleotide FASTA file of the input contig sequences
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pattern: "*.{fna}"
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- faa:
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type: file
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description: protein FASTA file of the translated CDS sequences
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pattern: "*.{faa}"
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- ffn:
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type: file
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description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)
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pattern: "*.{ffn}"
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- sqn:
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type: file
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description: an ASN1 format "Sequin" file for submission to Genbank
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pattern: "*.{sqn}"
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- fsa:
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type: file
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description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file
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pattern: "*.{fsa}"
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- tbl:
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type: file
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description: feature Table file, used by "tbl2asn" to create the .sqn file
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pattern: "*.{tbl}"
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- err:
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type: file
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description: unacceptable annotations - the NCBI discrepancy report.
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pattern: "*.{err}"
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- log:
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type: file
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description: contains all the output that Prokka produced during its run
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pattern: "*.{log}"
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- txt:
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type: file
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description: statistics relating to the annotated features found
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pattern: "*.{txt}"
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- tsv:
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type: file
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description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)
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pattern: "*.{tsv}"
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authors:
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- "@rpetit3"
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