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 |
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
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.
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.
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.
| 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. |
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.