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🔨 📐 Pipelines

This repo contains various analysis pipelines for the lab. Here are the basic rules:

  • each folder includes pipelines for a particular analysis - data type combination
  • pipelines are nextflow workflows
  • each pipeline comes with a list of conda environment files that manage the required software or a docker image that packages the required software

Data layout

Pipelines will usually operate from a top level project directory structured in the following way:

[project root]
├─ [pipeline].nf              # optional, see setup
├─ data                       # anything that is not code
│  ├─ raw
│  │  ├─ sample1_R1.fastq.gz
│  │  ├─ sample1_R2.fastq.gz
│  │  └─ ...
│  └─ ...
├─ figures
│  ├─ fig1.png
│  └─ ...
└─ refs                       # often a symbolic link
   ├─ eggnog
   └─ kraken2

The initial raw data lives in data/raw and all analysis artifacts should be written into data/ as well. Figures go into figures/.