This repository stores the code to reproduce the analysis of the project "The role of the thermodynamic pressure in Lensky's long-term evolution experiment"

To start this project clone this repo and do:

git clone https://github.com/alejandrogzi/thermut && cd thermut
./grouper.sh

to create the environment and build the population groups.

Your directory should now look like this:

...
├── groups
│   ├── m1.txt
│   ├── m2.txt
│   ├── m3.txt
│   ├── m4.txt
│   ├── m5.txt
│   ├── m6.txt
│   ├── m7.txt
│   ├── m8.txt
│   ├── p1.txt
│   ├── p2.txt
│   ├── p3.txt
│   ├── p4.txt
│   ├── p5.txt
│   ├── p6.txt
│   
...

Next, create the enviroment:

conda env create -f env.yml
conda activate thermut

Then, you are ready to run the pipeline:

nextflow run main.nf --dir /path/to/dir --meta /path/to/meta.csv --group /path/to/group.csv --gbk /path/to/gbk --fasta /path/to/fasta

Where:

• dir = directory containing fastq files
• meta = metadata file (./meta/metadata.txt)
• group = group file (a list of samples per population produced by ./grouper.sh)
• gbk = reference genbank file (./supp/REL606.6.gbk)
• fasta = reference fasta file (./supp/REL606.6.fasta)