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TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline
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'GEN3-DRS' is potentially outdated and not working #289

Closed angarb closed 2 years ago

angarb commented 2 years ago

@Vlad-Dembrovskyi

Problem

https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/a330894ee2cd7ece1191bde45f1961c65bf92505/main.nf#L284 1) The formatting of the manifest file changed: Old: image New (lacks Col1 = _subject_id/0 and the order changed): image md5sum, file_name, obj_id, file_size 2) In our script the tool we were using says it is here: https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/12a3227457e2cc287b6bb47bcba0924922ed5c3c/main.nf#L346 However, I can no longer follow that path: https://github.com/ga4gh/fasp-scripts/tree/master/scripts And it states that: "Note that as on 1st March 2021 these scripts have been superseded by Jupyter notebooks. Equivalent notebooks have been created in the notebooks folder, with numbering following that used here. A few scripts have not been migrated where newer services were available and the old script is no longer relevant. In the migration to some notebooks services were updated to new services - notably in the case of WES where more services are now available." We should investigate this further, but it is possible that @ianfore or @adeslatt can help us with this.

This problem was discovered while trying to:

  1. Run a job with an old manifest (Error message: No such file: gs://cloudosinputdata-jax-cloudos-12900/deploit/teams/xx/users/xx/projects/xx/jobs/xx/work/d7/xx/.command.env)
  2. Run a job with a new manifest (failed immediately)
angarb commented 2 years ago

As follow-up to the path question, we do have the fasp script containerized (and this is what the path points to).

If we ever need to find the path to Ian's script, it is currently here: https://github.com/ga4gh/fasp-scripts/blob/gtex/fasp/scripts/get_drs_url.py. This might also be relevant: https://github.com/ga4gh/fasp-scripts/tree/gtex/fasp/loc.

Our scripts are housed here (with slight modifications re Ian's script): https://github.com/lifebit-ai/fasp-scripts

However, the script itself was not an issue and the container worked. Other bugs were uncovered.