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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
3 KiB
YAML
91 lines
3 KiB
YAML
name: ncbigenomedownload
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description: A tool to quickly download assemblies from NCBI's Assembly database
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keywords:
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- fasta
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- download
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- assembly
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tools:
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- ncbigenomedownload:
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description: Download genome files from the NCBI FTP server.
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homepage: https://github.com/kblin/ncbi-genome-download
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documentation: https://github.com/kblin/ncbi-genome-download
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tool_dev_url: https://github.com/kblin/ncbi-genome-download
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doi: ""
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licence: ["Apache Software License"]
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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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- accessions:
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type: file
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description: List of accessions (one per line) to download
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pattern: "*.txt"
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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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- gbk:
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type: file
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description: GenBank format of the genomic sequence(s) in the assembly
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pattern: "*_genomic.gbff.gz"
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- fna:
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type: file
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description: FASTA format of the genomic sequence(s) in the assembly.
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pattern: "*_genomic.fna.gz"
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- rm:
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type: file
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description: RepeatMasker output for eukaryotes.
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pattern: "*_rm.out.gz"
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- features:
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type: file
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description: Tab-delimited text file reporting locations and attributes for a subset of annotated features
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pattern: "*_feature_table.txt.gz"
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- gff:
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type: file
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description: Annotation of the genomic sequence(s) in GFF3 format
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pattern: "*_genomic.gff.gz"
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- faa:
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type: file
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description: FASTA format of the accessioned protein products annotated on the genome assembly.
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pattern: "*_protein.faa.gz"
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- gpff:
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type: file
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description: GenPept format of the accessioned protein products annotated on the genome assembly.
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pattern: "*_protein.gpff.gz"
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- wgs_gbk:
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type: file
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description: GenBank flat file format of the WGS master for the assembly
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pattern: "*_wgsmaster.gbff.gz"
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- cds:
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type: file
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description: FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly
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pattern: "*_cds_from_genomic.fna.gz"
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- rna:
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type: file
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description: FASTA format of accessioned RNA products annotated on the genome assembly
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pattern: "*_rna.fna.gz"
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- rna_fna:
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type: file
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description: FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly
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pattern: "*_rna_from_genomic.fna.gz"
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- report:
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type: file
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description: Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly
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pattern: "*_assembly_report.txt"
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- stats:
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type: file
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description: Tab-delimited text file reporting statistics for the assembly
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pattern: "*_assembly_stats.txt"
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authors:
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- "@rpetit3"
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