Read Filtering

[BarryDigby]

The workflow would benefit from having an adapter trimming tool.

bbduk.sh should be installed in the container, use this tool to perform adapter trimming and read filtering. There are multiple parameters that can be passed to the bbduk.sh script which can be stored in the nextflow.config file (use sensible default parameters for users to overwrite).

You will also need to use conditionals in the script - we want to have the option to skip read filtering if re-running the workflow/working with cleaned reads as input.

To do

• Identify which parameters you will include in nextflow.config which the user can change to tweak trimming.
• Add the adapters.fa file to bin/adapters.fa. *
• Construct a basic nextflow script to perform trimming
• Add the boolean parameter trim_fastq to the nextflow.config and use as a conditional to run the processes.
• Add the boolean parameter save_trimmed_reads to the nextflow.config, use this in the publishDir directive.
• Once your test script is running, integrate to main.nf and open a PR.

---

For inspiration, you can inspect my circrna workflow which includes the features described above.

* A copy of the adatpers file is located here. Set this parameter as "${projectDir}/bin/adapters.fa" to stage the file in the workflow.