Execution Workflow: APAtrap

[ninsch3000]

WHAT

Write execution workflow for APAtrap. 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

  This BED file contains single-nucleotide position of poly(A) sites identified by the tool. Fields:

  chrom - the name of the chromosome chromStart - the starting position of the feature in the chromosome chromEnd - the ending position of the feature in the chromosome; as identified PAS are single-nucleotide, the ending position is the same as starting position name - defines the name of the identified poly(A) site score - not used, leave as "." strand - defines the strand; either "." (=no strand) or "+" or "-".

• [x] Output: Adhere to output specification for quantification challenge

  This BED file contains positions of unique poly(A) sites with TPM values for each identified site in the score column.

  chrom - the name of the chromosome chromStart - the starting position of the feature in the chromosome chromEnd - the ending position of the feature in the chromosome; as identified PAS are single-nucleotide, the ending position is the same as starting position name - defines the name of the identified poly(A) site score - TPM value for the identified site strand - defines the strand; either "." (=no strand) or "+" or "-".

• [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.

[SamBryce-Smith]

Hey @faricazjj

Just wanted to check if you're still going to be able to contribute to this workflow? Absolutely not a problem if not (though would be great if you still want to help out!), it's mainly so the rest of the group know what still needs to be done.

Also, if you've managed to make any progress so far it would be great to see any of your code pushed, even if it's still a work in progress! Most of all you'll get credit for your work but then others can join in too without starting from scratch.

Thanks :)

[faricazjj]

Hi @SamBryce-Smith ,

Thanks for checking in, I’ve been working on this workflow and am still working to complete it. Will push my code out this weekend :)

Cheers, Farica

On Fri, Jul 2, 2021 at 7:19 AM SamBryce-Smith @.***> wrote:

Hey @faricazjj https://github.com/faricazjj

Just wanted to check if you're still going to be able to contribute to this workflow? Absolutely not a problem if not (though would be great if you still want to help out!), it's mainly so the rest of the group know what still needs to be done.

Also, if you've managed to make any progress so far it would be great to see any of your code pushed, even if it's still a work in progress! Most of all you'll get credit for your work but then others can join in too without starting from scratch.

Thanks :)

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