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Don't include a sample if the sample name has a space #4

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florianzwagemaker opened this issue Jun 10, 2021 · 0 comments
Open

Don't include a sample if the sample name has a space #4

florianzwagemaker opened this issue Jun 10, 2021 · 0 comments
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enhancement New feature or request

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@florianzwagemaker
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Rewrite the regex rules to make sure that a sample will not be ran by the pipeline if a sample contains whitespace in its name:

Valid filename:
Example_data.fastq.gz

Invalid filename:
Example_data .fastq.gz (note the space between samplename and file extensions)

Change the regex to something like the following for nanopore data: ([ ]*)([\S]*)\.f(ast)?q(\.gz)?

  • Group 1 matches only if there's a space in the samplename, empty group if all is well.
  • Group 2 matches the actual sample name as long as there's no space in the sample name. Empty group if there's a space.
  • Group 3 & 4: matches the file extension(s)

Using these groups allows us to not include a sample in the samplesheet if it has a space in its name

@florianzwagemaker florianzwagemaker added bug Something isn't working enhancement New feature or request labels Jun 10, 2021
@florianzwagemaker florianzwagemaker removed the bug Something isn't working label Sep 9, 2021
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