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Required params

Problem

What params do I need to run the pipeline?

Bioinformatics pipelines require input of user data and settings. We have designed utia-gc/ngs and pipelines built on utia-gc/ngs to require limited params that are simple to specify.

Solution

We identified a few types of information that users must supply to be able to run the pipeline:

  • Input sample files
  • samplesheet -- Sample files and metadata formatted as a structured CSV file
  • Reference assembly information
  • genome -- A URL or path to a reference genome fasta file. May be gzip compressed.
  • annotations -- A URL path to a reference annotations GTF file. May be gzip compressed.

Usage