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Published 20 hours ago • verified publisher icon common-workflow-library

Create SnpSift_extract.cwl

Open cjuigne opened this issue 5 years ago • 2 comments

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

cjuigne avatar May 12 '20 13:05 cjuigne

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: cwltool SnpSift_extract.cwl --input_vcf test01.vcf --empty_text ' ' then the space is used correctly as a separator and not "eaten up" by the shell.

pvanheus avatar Oct 06 '20 11:10 pvanheus

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

cwl-bot avatar Oct 06 '20 13:10 cwl-bot