Create SnpSift_extract.cwl #75
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This part : - id: empty_text
type: string?
doc: "Represent empty fields with this value, rather than leaving them blank"
# inputBinding:
# prefix: -e
# position: 4
is commented because it doesn't work.
cf my issue on cwl.discourse : https://cwl.discourse.group/t/when-a-string-is-a-character-it-cant-be-enclosed-in-quotes/120
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Hi @hellymac I had a look at the issue you raised on discourse and things in fact (as @mr-c suggests) works as per the description. I.e. if I go: |
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This pull request has been mentioned on Common Workflow Language Discourse. There might be relevant details there: https://cwl.discourse.group/t/when-a-string-is-a-character-it-cant-be-enclosed-in-quotes/120/4 |
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| - id: extractFields | ||
| type: string[]? | ||
| default: "CHROM POS ID REF ALT FILTER" |
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This should be
default: ["CHROM", "POS", "ID", "REF", "ALT", "FILTER"]
| - id: empty_text | ||
| type: string? | ||
| doc: "Represent empty fields with this value, rather than leaving them blank" | ||
| # inputBinding: |
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This works as is and can be uncommented
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| stdout: $(inputs.input_vcf.nameroot).tsv | ||
| baseCommand: [SnpSift, -Xmx6G, extractFields] | ||
| arguments: |
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This is not necessary, you can use the empty_text field as specified below.
| doc: "SnpSift Extract Fields <http://snpeff.sourceforge.net/SnpSift.html#Extract> selects columns from a VCF dataset into a Tab-delimited format." | ||
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| stdout: $(inputs.input_vcf.nameroot).tsv | ||
| baseCommand: [SnpSift, -Xmx6G, extractFields] |
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Instead of specifying the RAM on the command line, compute it from runtime.ram, e.g.
baseCommand: [SnpSift]
arguments:
- "-Xmx$(runtime.ram)m"
- extractFields
and then add a ResourceRequirement to the requirements section, e.g.
requirements:
InlineJavascriptRequirement: {}
ResourceRequirement:
ramMin: 6000
| position: 4 | ||
| inputs: | ||
| - id: input_vcf | ||
| type: File |
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Consider specifying the format. VCF is EDAM format_3016, so put a format: edam:format_3016 here and a
$namespaces:
edam: http://edamontology.org/
$schemas:
- http://edamontology.org/EDAM_1.18.owl
at the end of the specification.
This part :
is commented because it doesn't work.
cf my issue on cwl.discourse : https://cwl.discourse.group/t/when-a-string-is-a-character-it-cant-be-enclosed-in-quotes/120