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Amanita jacksonii - NextFlow Genomics Pipeline

This is a NextFlow that will fully process a set of samples hosted on NCBI - SRA, piping them through

  • download,
  • trimming,
  • alignment, and
  • variant-calling

Expected CSV input

The pipeline expects a CSV table as input, specifically the SraRunTable.csv from NCBI-SRA.

Docker

Currently, the pipeline relies on docker to access containerized genomics packages for running specific modules.

It is expected that Docker desktop is installed previous to running the NextFlow pipeline. If running using MacOS, installing docker CLI using brew will also be required.

Run the pipeline locally

The pipeline can be run simply by invoking the run.sh command (which expect the CSV samples table as input)

bash run.sh

data output directory configuration

The pipeline will output to data directory, which is ignored by git.

data
  |--- samples
  |       |------ SraRunTable.csv
  |
  |--- fastq
  |      |------ SRRXXXX_1.fastq.gz
  |      |------ SRRXXXX_2.fastq.gz
  |
  |--- bam
  |     |-------- SRRXXXX_merged.bam
  |     |-------- SRRXXXX_merged.bam.bai
  |
  |--- genome
          |------ ref_genome.fasta.gz
          |------ ref_genome.fasta.gz.*