trim.rules¶

The trim.rules workflow performs FASTQ trimming to remove poor quality sequences and technical sequences such as adapters. It should be used with high-coverage genomic DNA.
The pipeline contains the rules for trimming fastq files using Trimmomatic in a Snakemake workflow.

The rules in this file perform the following tasks: - Import necessary libraries and modules - Read the configuration file - Define wildcard constraints for prefixes and samples - Define a function to get the fastq files for a given prefix - Define a function to get the trimmed fastq files for a given prefix - Define the 'trim' rule which specifies the input, output, log, benchmark, parameters, and wrapper for the Trimmomatic tool

Pipeline overview¶

• You have downloaded FASTQ Data to a subdirectory within a data directory.
• You have filled out the config_main.yaml file with the appropriate information.
• You have installed base snakemake environment using conda env create -f envs/snake_env.yaml and activated it using conda activate snake_env

Usage¶

Testing the pipeline on IBU¶

This command uses a test dataset

snakemake -np -s workflow/trim.rules --profile slurm 2>&1 | tee logs/log_trim.txt

Running the pipeline on IBU¶

Note: if you are having issues running Snakemake or need reminders, check out the Snakemake page.

snakemake -s workflow/trim.rules --profile slurm 2>&1 | tee logs/log_trim.txt