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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:
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)
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
The text was updated successfully, but these errors were encountered:
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
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:
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)Expected behavior
The --dry-run flag should report all files that will be downloaded
The text was updated successfully, but these errors were encountered: