sequana-bioconvert 1.2.0

Installation

pip install sequana-bioconvert

To upgrade an existing installation:

pip install sequana-bioconvert --upgrade

Install all dependencies via conda/mamba:

mamba env create -f environment.yml

Quick Start

Step 1 — prepare the working directory

Convert all fastq.gz files in a directory to fasta.gz:

sequana_bioconvert \
    --input-directory /path/to/data \
    --input-ext fastq.gz \
    --output-ext fasta.gz \
    --command fastq2fasta

This creates a bioconvert/ working directory with config.yaml and a bioconvert.sh launch script.

Step 2 — run the pipeline:

cd bioconvert
sh bioconvert.sh

Results are written to the output/ subdirectory. An HTML summary report is generated on completion.

Usage

sequana_bioconvert --help

Key options:

• --input-directory — directory containing the input files (required)

• --input-ext — extension of input files, e.g. fastq.gz (required)

• --output-ext — extension of output files, e.g. fasta.gz (required)

• --command — bioconvert conversion command, e.g. fastq2fasta (required);

  run bioconvert --help for the full list

• --input-pattern — prefix glob to restrict which files are picked up (default: *);

  e.g. sample_* to process only files starting with sample_

• --method — override the default conversion method;

  run bioconvert COMMAND --show-methods to list valid methods

Usage with apptainer

All external tools are available through a pre-built apptainer image. To use it, add --use-apptainer when initialising the pipeline:

sequana_bioconvert \
    --input-directory /path/to/data \
    --input-ext fastq.gz \
    --output-ext fasta.gz \
    --command fastq2fasta \
    --use-apptainer \
    --apptainer-prefix ~/.sequana/apptainers

Then run as usual:

cd bioconvert
sh bioconvert.sh

Requirements

• bioconvert ≥ 1.1.0 — the underlying conversion tool

• graphviz — for pipeline DAG rendering (available via apptainer)

Install dependencies via conda/mamba:

mamba env create -f environment.yml

Rules and configuration details

The latest configuration file is available at: config.yaml

Each rule used in the pipeline has a corresponding section in config.yaml.

Changelog

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.