stjude-dnb-binfcore / sc-rna-seq-snap

BSD 2-Clause "Simplified" License

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Add all scripts to run cellranger-analysis module #13

Closed AntoniaChroni closed 5 hours ago

AntoniaChroni commented 1 week ago

Purpose/implementation Section

Type of change

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update.

What scientific question/module of analysis is your analysis addressing?

To run and summarize Cell Ranger count for single or multiple libraries for sc-/sn-RNA-Seq Analysis in 10X Genomics data across the project.

What GitHub issue does your pull request address?

Closes #12. Closes #17. Closes #16.

Directions for reviewers

Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run:

[x] submit-multiple-jobs.sh

Instructions on how to run the file can be found in the README file.

Is there anything that you want to discuss further?

Please also confirm the following:

[x] README file contains enough clear documentation on running the module.
[x] Review the code on the j1.sh file for clarity.
[x] Review the code on the j2.sh file for clarity.
[x] Review the code on the submit-multiple-jobs.sh file for clarity.
[x] Review the code on the waiter.sh file for clarity.
[x] Review the code on the ./util/run_cellranger.py file for clarity.
[x] Review the code on the summarize_cellranger_results.py file for clarity.

Results

What was your approach?

Here we use CellRanger v8.0.1 and run by default parameters, i.e., there are no constraints to the number of cells to be considered per library.

Reproducibility Checklist

[ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.

Documentation Checklist

[x] This analysis module has a README and it is up to date.
[x] The analytical code is documented and contains comments.

AntoniaChroni commented 6 hours ago

@sharonfreshour Everything has been updated accordingly. Just so you know – suggestions not being directly accepted have been done at once here 0c2d72aa23ca80abb9ee52afdb371b91ad297299.