sequana-bioconvert 1.1.0

description: convert NGS format from one to another using bioconvert

This is is the bioconvert pipeline from the Sequana project

Overview:

convert NGS format from one to another using Bioconvert

Input:

whatever input format accepted by Bioconvert

Output:

whatever output format accepted by Bioconvert

Status:

production

Citation:

Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352

Installation

This package depends on Python only and singularity. To install sequana_bioconvert, just install this package as follows:

pip install sequana_bioconvert

For singularity, we recommend to use a conda environment:

conda create --name bioconvert -y python=3.8 singularity
conda activate bioconvert
pip install sequana_bioconvert

Usage

sequana_bioconvert --help

You need to provide the type of conversion you wish to perform with the –command argument. You also need to tell the type of extensions expected including the compression (gz, bz2 or dsrc recognised). Finally, the –input-directory and –input-pattern must be used to find the input files.:

sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext
    fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"

This command creates a directory with the pipeline and configuration file. You will then need to execute the pipeline as follows:

cd bioconvert
sh bioconvert.sh  # for a local run

This launches a snakemake pipeline. Symbolic links to the input data are created in the ./input directory and results stored in the ./output directory.

Some conversions require external standalones. We recommend to use our singularity image. To do so, add –use-apptainer options when you initialse the pipeline. You can also specify where to store the singularity image once for all using –apptainer-prefix:

sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext
    fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"
    --use-apptainer --apptainer-prefix ~/images

See bioconvert.readthedocs.io for more details about bioconvert itself.

If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:

snakemake -s bioconvert.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s) installed with sequana_bioconvert: bioconvert

All dependencies and external dependencies related to bioconvert are available through the apptainer used by this sequana_bioconvert pipeline.

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Version	Description
1.0.0	Uses bioconvert 1.0.0
0.10.0	Add container
0.9.0	Version using new sequana/sequana_pipetools framework
0.8.1	Working version
0.8.0	First release.

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.