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description: convert NGS format from one to another using bioconvert

Project description

This is is the bioconvert pipeline from the Sequana project

Overview:TODO
Input:TODO
Output:TODO
Status:draft
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

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_bioconvert

Usage

sequana_pipelines_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 creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd bioconvert
sh bioconvert.sh  # for a local run

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

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):

  • bioconvert
https://raw.githubusercontent.com/sequana/sequana_bioconvert/master/sequana_pipelines/bioconvert/dag.png

Details

This pipeline runs bioconvert in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.

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
0.8.1 Working version
0.8.0 First release.

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