Execution Workflow: APAlyzer

iRNA-COSI / APAeval

Community effort to evaluate computational methods for the detection and quantification of poly(A) sites and estimating their differential usage across RNA-seq samples

MIT License

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Execution Workflow: APAlyzer #19

Closed ninsch3000 closed 2 years ago

ninsch3000 commented 3 years ago

WHAT

Write execution workflow for APAlyzer. Use the provided small files for testing (running the workflow on real data is a different issue).

CHECKLIST

[x] Use snakemake template or nextflow template to create your workflow.
[x] Comment your code
[x] Run individual rules/processes in either conda envs or docker/singularity containers for reproducibility
[x] Input: .bam or .fastq from test_data
[ ] Give feedback about the method

OUTPUTS (see specification):

[x] ~Output: Adhere to output specification for Identification challenge~ (No identification)
[x] ~Output: Adhere to output specification for quantification challenge~ (No quantification)
[x] Output: Adhere to output specification for differential usage challenge
This TSV file contains two columns:
- gene ID
- significance of differential PAS usage
Column names should not be added to the file.

mkatsanto commented 3 years ago

I have created the following branch https://github.com/iRNA-COSI/APAeval/tree/apalyzer APAlyzer implementation is currently stuck since the creation of a reference genome based on a given gtf is not working for this tool. You currently have to rely on predefined PAS atlas, which is not reliable for the benchmark. I opened an issue in the git repo of the tool (https://github.com/RJWANGbioinfo/APAlyzer/issues/7) and await further info.

SamBryce-Smith commented 3 years ago

@mkatsanto looks like issue you've reported has been fixed. Are you still able to carry on with completing this workflow (looks like you've done a lot already!) or should we consider this workflow open for other contributors?

Thanks :)

SamBryce-Smith commented 3 years ago

Hey @mkatsanto, do you think you'll find the time to finish this off over the next couple of weeks or should I reassign the workflow to someone else?

mkatsanto commented 3 years ago

Hi! Sorry for the late reply! I will try in the next week to resolve it . If someone wants to also take a try or work also on this, it is fine by me.

SamBryce-Smith commented 3 years ago

Hey @mkatsanto, just a gentle bump on this workflow. We've got a deadline of 30th September for getting the execution workflows merged, do you think you'll have time to finish it off?