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chanzuckerberg / idseq-workflows

Portable WDL workflows for IDseq production pipelines
https://idseq.net/
MIT License
31 stars 12 forks source link

handle spaces in cg sample names #152

Closed morsecodist closed 2 years ago

morsecodist commented 2 years ago

This will allow these file names to have spaces without breaking stuff.

rzlim08 commented 2 years ago

Looks good for Illumina, is it in scope to get this working for ONT pipelines? Looks like it may be more complex.

morsecodist commented 2 years ago

@rzlim08 why so? I looked through every instance of ~{sample} and they are all within quotes already. The only problem (I think) is that ZipOutputs takes arbitrary output paths from other steps and doesn't use quotes.

rzlim08 commented 2 years ago

@rzlim08 why so? I looked through every instance of ~{sample} and they are all within quotes already. The only problem (I think) is that ZipOutputs takes arbitrary output paths from other steps and doesn't use quotes.

Looks like the problem is happens when it gets passed to the artic pipeline (RunMinion), which is why it might be a bit more complex.