Скачать или смотреть How to Use Snakemake to Process Multiple Samples with Porechop Correctly

Learn how to effectively implement `Porechop` in your `Snakemake` workflow to process multiple FASTQ files without errors.
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This video is based on the question https://stackoverflow.com/q/68486202/ asked by the user 'a_riou' ( https://stackoverflow.com/u/16501156/ ) and on the answer https://stackoverflow.com/a/68496156/ provided by the user 'dariober' ( https://stackoverflow.com/u/1114453/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions.

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Efficiently Using Snakemake with Porechop to Process Multiple Samples

If you're working with multiple DNA sequencing data files, using a workflow management tool like Snakemake can greatly streamline your data processing. However, challenges often arise when trying to handle multiple inputs within rules, especially when using tools like Porechop. In this guide, we'll explore a common problem and solution for successfully implementing Porechop in a Snakemake pipeline to process multiple FASTQ files without encountering errors.

The Problem: Handling Multiple Inputs

A user encountered an issue while using Porechop in a Snakemake workflow. Despite having formatted the workflow to process several samples, the command executed only once for all input files rather than separately for each one. This resulted in an error indicating that one command exited with a non-zero exit code.

Here's a summary of the situation:

Data Structure: Multiple FASTQ files (e.g., sample1.fastq.gz, sample2.fastq.gz).

Expected Behavior: The command should run multiple times, each time for one file.

Actual Behavior: The command ran once, attempting to process all files at once, leading to failure.

This is a common problem that many users face when they inadvertently feed a list of files to a rule rather than specifying individual files for processing.

Understanding the Solution

The root of the problem lies in how the input and output are defined within the Porechop rule. Here’s how we can resolve the issue and ensure that each sample is processed correctly.

Simplifying the Rule Structure

To run Porechop on each input file without conflicts, you need to remove the expand() function from the input: and output: sections of the porechop rule. By doing so, each sample is treated individually. Here’s how to adjust your rule:

Before - Incorrect Implementation

[[See Video to Reveal this Text or Code Snippet]]

After - Correct Implementation

[[See Video to Reveal this Text or Code Snippet]]

Key Changes Explained

Input Specification:

By using DIR_FASTQ+ "{sample}.fastq.gz" instead of expand, you tell Snakemake to process each sample file separately.

Output Specification:

Similar to input, using "/ngs/prod/nanocea_project/test/prod/porechop/{sample}_pore.fastq.gz" ensures that there's an individual output for each processed sample.

This change clarifies to Snakemake that each sample should be handled independently, avoiding the error associated with running the command on multiple files at once.

Conclusion

When using Snakemake with tools like Porechop, understanding how to define your rules is crucial for ensuring that your workflow processes files as expected. By simplifying the structure of your rules and removing the unnecessary expand() function, you can effectively process multiple samples without encountering execution errors.

Feel free to refer back to this post whenever you run into challenges setting up your workflow, and happy coding!