Add nextclade tool (nextstrain/nextclade) #101
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| #!/usr/bin/env cwl-runner | ||
| cwlVersion: v1.0 | ||
| class: CommandLineTool | ||
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| doc: Assign Nextstrain clades to SARS-CoV-2 sequences and provide QC information | ||
| id: nextclade | ||
| label: Nextclade | ||
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| dct:creator: | ||
| "@id": "https://orcid.org/0000-0001-6553-5274" | ||
| foaf:name: Peter van Heusden | ||
| foaf:mbox: "mailto:pvh@sanbi.ac.za" | ||
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| requirements: | ||
| DockerRequirement: | ||
| dockerPull: neherlab/nextclade:0.8.1-alpine | ||
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| hints: | ||
| ResourceRequirement: | ||
| coresMin: 1 | ||
| ramMin: 512 # 512 MB | ||
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| inputs: | ||
| input_fasta: | ||
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| type: File | ||
| doc: .fasta or .txt file with input sequences | ||
| format: | ||
| - edam:format_1929 # FASTA | ||
| - edam:format_1964 # plain text format | ||
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| inputBinding: | ||
| prefix: --input-fasta | ||
| input_qc_config: | ||
| type: File? | ||
| doc: QC config json file containing custom QC configuration | ||
| format: edam:format_3464 # JSON | ||
| inputBinding: | ||
| prefix: --input-qc-config | ||
| input_root_seq: | ||
| type: File? | ||
| doc: plain text file containing custom root sequence | ||
| format: edam:format_1964 | ||
| inputBinding: | ||
| prefix: --input-root-seq | ||
| input-tree: | ||
| type: File? | ||
| doc: Auspice JSON v2 file containing custom reference tree | ||
| format: edam:format_3464 | ||
| inputBinding: | ||
| prefix: --input-tree | ||
| input-gene-map: | ||
| type: File? | ||
| doc: 'JSON file containing custom gene map. Gene map (sometimes also called "gene annotations") is used to resolve aminoacid changes in genes.' | ||
| format: edam:format_3464 | ||
| inputBinding: | ||
| prefix: --input-gene-map | ||
| input-pcr-primers: | ||
| type: File? | ||
| doc: CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites. | ||
| format: edam:format_3572 | ||
| inputBinding: | ||
| prefix: --input-pcr-primers | ||
| output_options: | ||
| type: | ||
| type: record | ||
| name: output_options_record | ||
| fields: | ||
| output_json_filename: | ||
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There was a problem hiding this comment. Do all of these filenames need to be specified by the user? Why not take the name root of the FASTA and add the relevant file extension? There was a problem hiding this comment. The underlying tool has options for different output names for each output file. While I am not sure if that will be used in practice, I have followed the underlying tool in the CWL here. There was a problem hiding this comment. Nextclade dev here. Let us know, folks, what would be the most convenient set of flags. We are flexible here. There was a problem hiding this comment. For "user" I meant the user of this CWL description. For nextclade itself @ivan-aksamentov you did the correct thing to ask for the filename/path. Is there a cost to output all these types? @pvanheus If not then I recommend always requesting all output types via the There was a problem hiding this comment. Good point: from a workflow point of view, naming of files is not relevant. @ivan-aksamentov if i understand correctly the outputs are typically small and there is no significant cost to asking for all of them? |
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| type: string? | ||
| doc: Filename of output JSON results file | ||
| inputBinding: | ||
| prefix: --output-json | ||
| output_csv_filename: | ||
| type: string? | ||
| doc: Filename of output CSV results file | ||
| inputBinding: | ||
| prefix: --output-csv | ||
| output_tsv_filename: | ||
| type: string? | ||
| doc: Filename of output TSV results file | ||
| inputBinding: | ||
| prefix: --output-tsv | ||
| output_tsv_clades_only_filename: | ||
| type: string? | ||
| doc: Filename to output CSV clades-only file | ||
| inputBinding: | ||
| prefix: --output-tsv-clades-only | ||
| output_tree_filename: | ||
| type: string? | ||
| doc: Filename of output Auspice v2 tree file | ||
| inputBinding: | ||
| prefix: --output-tree | ||
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| outputs: | ||
| output_json: | ||
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| type: File? | ||
| format: edam:format_3464 | ||
| outputBinding: | ||
| glob: $(inputs.output_options.output_json_filename) | ||
| output_csv: | ||
| type: File? | ||
| format: edam:format_3572 # Comma-separated values | ||
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| outputBinding: | ||
| glob: $(inputs.output_options.output_csv_filename) | ||
| output_tsv_clades_only: | ||
| type: File? | ||
| format: edam:format_3475 # Tab-separated values | ||
| outputBinding: | ||
| glob: $(inputs.output_options.output_tsv_clades_only_filename) | ||
| output_tsv: | ||
| type: File? | ||
| format: edam:format_3475 | ||
| outputBinding: | ||
| glob: $(inputs.output_options.output_tsv_filename) | ||
| output_tree: | ||
| type: File? | ||
| format: edam:format_3464 | ||
| outputBinding: | ||
| glob: $(inputs.output_options.output_tree_filename) | ||
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| baseCommand: [ nextclade.js ] | ||
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| $namespaces: | ||
| edam: http://edamontology.org/ | ||
| dct: http://purl.org/dc/terms/ | ||
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| foaf: http://xmlns.com/foaf/0.1/ | ||
| $schemas: | ||
| - http://edamontology.org/EDAM_1.18.owl | ||
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| input_fasta: | ||||||
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| class: File | ||||||
| format: edam:format_1929 | ||||||
| location: https://bigd.big.ac.cn/ncov/genome/sequence/download/single/MT981459 | ||||||
| output_options: | ||||||
| output_json_filename: MT981459.json | ||||||
| output_csv_filename: MT981459.csv | ||||||
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| $namespaces: | ||||||
| edam: http://edamontology.org/ | ||||||
| $schemas: | ||||||
| - http://edamontology.org/EDAM_1.18.owl | ||||||
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No need for
idhere