nextflow-riboseqc

A single-file basic nextflow pipeline to perform Ribosome profiling quality control using RiboseQC R package.

Test data

To obtain test data:

1. Download the original RiboseQC test test_human_HEK293.bam file using this link and place it into the test_data subdirectory.
2. Run test_data/make_test_data.sh to regenerate the annotation.

How to run

nextflow run . -profile local,docker will run the pipeline on test data locally (prerequisite: docker rights).

It will generate results folder with the results of the analysis.

For debugging, use nextflow run . -profile local,docker -resume.

Run on your data

To run on your data, you need to specify the following parameters:

input_dir : directory containing aligned bam files of the riboseq data gtf : unzipped gtf file of your annotation fasta : unzipped genome sequence of your annotation

Optionally, specify output directory with --outdir (default: results).

nextflow run slebedeva/nextflow-riboseqc \
--input_dir $INPUT_DIR \
--gtf $GTF \
--fasta $FASTA