billgreenwald / nextflow_ase_pipeline

A nextflow pipeline to deploy and run WASP and samtools to obtain allele specific effects summary files

Nextflow ASE Pipeline

A Nextflow pipeline to use samtools and WASP to get ASE summary data.

Usage:

1. Set the variables within the ase_pipeline.nf file in the Configuration for the specific run section, and anything needed for the pipeline.

2. External programs are not included, but can be downloaded publicly and added to a "/bin" folder. They should be: -WASP -your aligner -Samtools

3. Edit the ase_pipeline.nf process 'remap' to match your aligner and the arguments for the aligner.