This pipeline takes some BAM files from ICGC and runs featureCounts on them.
ICGC-FeatureCounts: This pipeline takes some BAM files from ICGC and runs featureCounts on them.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The ICGC-FeatureCounts pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
This pipeline was written by Alexander Peltzer (apeltzer) at QBiC.