feat(Execution workflow): APA-Scan

WHAT

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

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

[ ] 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 "-".
[ ] 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 "-".
[ ] Can APA-Scan do differential PAS quantification? If yes:
[ ] 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.