NanoCLUST_runner

Python script that runs NanoCLUST on files in a directory with only 1 command.

Introduction

With the NC_runner.py script, you only have to enter a command once! The script starts a NanoCLUST run for files with a specified suffix in a directory you choose.

This script was developed because NanoCLUST often has to be used on multiple fastq files, but using wildcards to select multiple files doen't work optimally.

Usage

1. Download the NC_runner.py script to a usefull location (preferably your home directory to avoid mistakes in the path)
2. Add the absolute paths for your database and taxdatabase to the argparse default part of the script (reduces the length of your commands and avoids mistakes in the paths)
3. Add the path to the main.nf file from NanoCLUST to the argparse default part of the script
4. Optional: Change the default output directory location to something usefull
5. Optional: Change the default suffix from the argparse part of the script to a suffix you will often use
6. Run the script!

If there is no input directory specified, or the input directory does not exist, the script will exit.

If the output direcotry does not exist, the script will notify you and create it.

Output

The outputs of NanoCLUST will be placed in the output directory you specified, or in your current working directory (default). For each NanoCLUST run, a separate folder will be created with the name of the corresponding sample. Those folders contain the 3 output directories (classification data, fastqc results, pipeline info) created by NanoCLUST.

Example commands

Basic command, only input directory specified (default settings):

python NC_runner.py sequencedata 

Input and output directory, file suffix specified

python NC_runner.py sequencedata -o NanoCLUST_out -s .fastq.gz

Input and output directory, file suffix, main.nf path specified

python NC_runner.py sequencedata -o NanoCLUST_out -s .fastq.gz -n project1/programs/NanoCLUST/main.nf

Input and output directory, file suffix, main.nf path, database paths specified

python NC_runner.py sequencedata -o NanoCLUST_out -s .fastq.gz -n project1/programs/NanoCLUST/main.nf -d project1/db/16S_ribosomal_RNA -t project1/db/taxdb