✨ Add liftover and collapse workflow #337
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📝 updated docs 🔧 fixed bugs 🐎 parrallel gzip of files
🔧 fixed hint 📝 Updated readme
migbro
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📝 edited readme to reflect changes ➖ dropped superfluous shell script
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Co-authored-by: Dan Miller <dmiller15@users.noreply.github.com>
🔨 wf refactor
🏆 address PR concerns and suggestions
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|
Got an updated task: https://cavatica.sbgenomics.com/u/brownm28/playground/tasks/2990d1eb-57d3-4fce-9be2-33f026049e1d/# |
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Merging without GA, since this is not being run in GA. |
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Purpose/implementation Section
What scientific question is your analysis addressing?
How to make older RNA expression datasets compatible with new ones
What was your approach?
Lifttover using a GTF, leave genes alone that weren't in the GTF, collapse repeat symbols on highest row mean
What GitHub issue does your pull request address?
d3b-center/ticket-tracker-OPC#521
and
d3b-center/ticket-tracker-OPC#522
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
You can use this task https://cavatica.sbgenomics.com/u/brownm28/playground/tasks/8df870cc-69b0-4b44-a55e-205af9c7c874/ to see an example.
Is there anything that you want to discuss further?
In practice, use the gencode 39 gtf, and name the output file appropriately. Do I need to do something with circleci?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes - readme helps as well
Results
What types of results are included (e.g., table, figure)?
Outputs
What is your summary of the results?
They look great, and line count using v36 as a gold standard from task https://cavatica.sbgenomics.com/u/d3b-bixu-ops/open-target-tcga-rnaseq-counts/tasks/580834b3-cb6a-4ac1-b188-826aef4203dc/ is the same
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.