Feature/update manifest

ASAP-CRN / harmonized-wf-dev

Repo for testing and developing a common postmortem-derived brain sequencing (PMDBS) workflow harmonized across ASAP

Apache License 2.0

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Feature/update manifest #54

Open kfang4 opened 4 months ago

kfang4 commented 4 months ago

Remove multiome docker image (used in R version of workflow)
Remove path from output files in manifest files
Currently, we write manifest workflows with the subworkflow and subworkflow_version, but instead, write them with the whole workflow. This means that another variable needs to be updated when workflow is updated (preprocess version, cohort analysis version, workflow version). Example:
```
filename    timestamp      workflow              workflow_version      workflow_release
f.tsv       2024-06-04..   harmonized_pmdbs      v2.1.0                https://github.com/ASAP-CRN/harmonized-wf-dev/releases/tag/harmonized_pmdbs_analysis-v2.1.0
```

kfang4 commented 3 months ago

~~To do:~~ ~~- Add file checksums into the manifest (and the metadata files, generated upon file upload)~~

filename    md5_hash                      timestamp      workflow              workflow_version      workflow_release
f.tsv       JKE1rykVi8qPd/7BclJNnQ==      2024-06-04..   harmonized_pmdbs      v2.1.0                https://github.com/ASAP-CRN/harmonized-wf-dev/releases/tag/harmonized_pmdbs_analysis-v2.1.0

kfang4 commented 3 months ago

To note for promote_staging_data script:

Changes in feature/update-manifest include renaming workflow to just harmonzied_pmdbs rather than preprocess and cohort_analysis in manifest files
Changes in feature/update-manifest include adding hash (md5) in manifest files
Changes in feature/update-manifest include adding the GitHub release link in manifest files