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cubi-tk snappy pull-raw-data --dry-run only reports fastq files that match the library name #194

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Nicolai-vKuegelgen opened this issue Sep 19, 2023 · 0 comments

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@Nicolai-vKuegelgen
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Describe the bug
When using cubi-tk snappy pull-raw-data with the --dry-run option a report is created that lists the number of (fastq) files that will be downloaded. However, contrary to what is actually downloaded without dry-run this list only contains files whose name matches the sample/library name of the collection in which the files are placed.

To Reproduce
Steps to reproduce the behavior:

  1. Run cubi-tk snappy pull-raw-data --dry-run on any project / collection where the fastq file names do not match library names (i.e. because the where sequenced externally and - as is proper - not renamed prior to Sodar upload)
  2. The reported list of files will be incomplete (or even fully empty).

Expected behavior
The --dry-run flag should report all files that will be downloaded

@Nicolai-vKuegelgen Nicolai-vKuegelgen changed the title cubi-tk snappy pull-raw-data --dry-run only reporst fastq files that match the library name cubi-tk snappy pull-raw-data --dry-run only reports fastq files that match the library name Sep 19, 2023
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