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Introduce minimal Schema for nanopore registration #350

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Merged
Steffengreiner merged 8 commits into from
Feb 13, 2023
Merged

Introduce minimal Schema for nanopore registration #350

Steffengreiner merged 8 commits into from
Feb 13, 2023

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@Steffengreiner Steffengreiner commented Jan 31, 2023 •
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What was changed
This PR introduces a schema and example json for checking if the minimal required files for a nanopore data registration are within a provided dataset.
Additionally it adapts the OxfordNanoporeExperiment generation to not fail if an unknown file or folder is found but include them as OptionalFile and OptionalFolder in the datastructure to allow for variations within the provided datastructure.

Background information
As of now the minimum required folders are:

  • FASTQ_FAIL
  • FASTQ_PASS
  • FAST5_FAIL
  • FAST5_PASS

While the minimum required files are:

  • final_summary.txt (We extract metadata from this file)
  • report.md (We extract metadata from this file)
  • sequencing_summary.txt (Both Labs)

Open Questions
Due to the new constraints, the previously defined schemas and datafiles/Datafolders are ALL now unnecessary and could be deleted, since as soon as the minimal required files are provided the OxfordNanoporeExperiment is created and can be parsed.
The only reason for keeping multiple schemas could be if the distinction between the files in the OxfordnanoporeExperiment class is necessary (e.g. for accessing metadata within the files).
However this is only the case for the final_summary.txt file and the report.md file as of yet.

Steffengreiner added 2 commits January 30, 2023 17:25
@Steffengreiner Steffengreiner requested a review from a team as a code owner January 31, 2023 12:42
@Steffengreiner Steffengreiner mentioned this pull request Jan 31, 2023
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KochTobi
KochTobi requested changes Feb 13, 2023
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Only some minor requests

KochTobi
KochTobi approved these changes Feb 13, 2023
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LGTM 👍

@Steffengreiner Steffengreiner merged commit d0a192a into development Feb 13, 2023
@Steffengreiner Steffengreiner deleted the feature/dm-669-valid-minimal-nanopore-datastructure branch February 13, 2023 13:58
Steffengreiner added a commit that referenced this pull request Feb 13, 2023
@Steffengreiner
Merge pull request #354 from qbicsoftware/development
bf0a815 
Introduce minimal Schema for nanopore registration  (#350)
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@Steffengreiner @KochTobi