.. image:: https://badge.fury.io/py/sequana-depletion.svg
:target: https://pypi.python.org/pypi/sequana_depletion
.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
:alt: JOSS (journal of open source software) DOI
.. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/depletion/actions/workflows
This is is the **depletion** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
:Overview: select or deplete reads from input FastQ files given a reference
:Input: Fastq Files
:Output: Fastq Files
: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
~~~~~~~~~~~~
Install this package as follows::
pip install sequana_depletion
it requires https://sequana.readthedocs.io and https://bioconvert.readthedocs.io for the bam to fastq conversion
Usage
~~~~~
::
sequana_depletion --help
sequana_depletion --input-directory DATAPATH --reference hg38.fa --mode depletion
sequana_depletion --input-directory DATAPATH --reference covid.fa --mode selection
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::
cd depletion
sh depletion.sh # for a local run
This launch a snakemake pipeline. 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 depletion.rules -c config.yaml --cores 4 --stats stats.txt
Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- bwa
- samtools
- bamtools
#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png
Details
~~~~~~~~~
This pipeline runs **depletion** 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 <https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
Changelog
~~~~~~~~~
========= ====================================================================
Version Description
========= ====================================================================
0.3.0 * use click and new sequana_pipetools. convert to pyproject
0.2.0 * handle paired/unpaired data
* refactorise to use containers/apptainers
0.1.0 **First release.**
========= ====================================================================
Raw data
{
"_id": null,
"home_page": "https://github.com/sequana/depletion",
"name": "sequana-depletion",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.8,<4.0",
"maintainer_email": "",
"keywords": "snakemake,sequana,depletion,NGS",
"author": "Sequana Team",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/f6/39/8c30ca4d2fd8e69b942f8151b1bdb67aeafd6dfa208c7f1a1e5f6c903287/sequana_depletion-0.3.0.tar.gz",
"platform": null,
"description": "\n.. image:: https://badge.fury.io/py/sequana-depletion.svg\n :target: https://pypi.python.org/pypi/sequana_depletion\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n :target: http://joss.theoj.org/papers/10.21105/joss.00352\n :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/depletion/actions/workflows \n\n\n\n\nThis is is the **depletion** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project\n\n:Overview: select or deplete reads from input FastQ files given a reference\n:Input: Fastq Files\n:Output: Fastq Files\n:Status: production\n:Citation: Cokelaer et al, (2017), \u2018Sequana\u2019: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\nInstall this package as follows::\n\n pip install sequana_depletion\n\nit requires https://sequana.readthedocs.io and https://bioconvert.readthedocs.io for the bam to fastq conversion\n\n\nUsage\n~~~~~\n\n::\n\n sequana_depletion --help\n sequana_depletion --input-directory DATAPATH --reference hg38.fa --mode depletion\n sequana_depletion --input-directory DATAPATH --reference covid.fa --mode selection\n\nThis creates a directory with the pipeline and configuration file. You will then need\nto execute the pipeline::\n\n cd depletion\n sh depletion.sh # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can\nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n snakemake -s depletion.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- bwa\n- samtools\n- bamtools\n\n#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **depletion** in parallel on the input fastq files (paired or not). \nA brief sequana summary report is also produced.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/config.yaml>`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. \n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion Description\n========= ====================================================================\n0.3.0 * use click and new sequana_pipetools. convert to pyproject\n0.2.0 * handle paired/unpaired data\n * refactorise to use containers/apptainers\n0.1.0 **First release.**\n========= ====================================================================\n\n\n\n",
"bugtrack_url": null,
"license": "BSD-3",
"summary": "A pipeline to deplete reads from a given reference",
"version": "0.3.0",
"project_urls": {
"Homepage": "https://github.com/sequana/depletion",
"Repository": "https://github.com/sequana/depletion"
},
"split_keywords": [
"snakemake",
"sequana",
"depletion",
"ngs"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "63648c0900ae60782194bc913ce756a87a881e8db74fa68a59395e9c63c86fa4",
"md5": "bbf8128e0533d05b1b11336f116027d0",
"sha256": "474373de3fcec58676b4f42eb68c081a4bc2383a60d2a67d9a5eca61cd2d7243"
},
"downloads": -1,
"filename": "sequana_depletion-0.3.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "bbf8128e0533d05b1b11336f116027d0",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8,<4.0",
"size": 8030,
"upload_time": "2023-12-17T09:17:41",
"upload_time_iso_8601": "2023-12-17T09:17:41.042496Z",
"url": "https://files.pythonhosted.org/packages/63/64/8c0900ae60782194bc913ce756a87a881e8db74fa68a59395e9c63c86fa4/sequana_depletion-0.3.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "f6398c30ca4d2fd8e69b942f8151b1bdb67aeafd6dfa208c7f1a1e5f6c903287",
"md5": "a67cad72a22ec0bab5bdef2c57d3106b",
"sha256": "8c5cd1a2972e7517319a993731ada01ffd595e160b3c4fdfac74f8699a246232"
},
"downloads": -1,
"filename": "sequana_depletion-0.3.0.tar.gz",
"has_sig": false,
"md5_digest": "a67cad72a22ec0bab5bdef2c57d3106b",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8,<4.0",
"size": 5866,
"upload_time": "2023-12-17T09:17:42",
"upload_time_iso_8601": "2023-12-17T09:17:42.029525Z",
"url": "https://files.pythonhosted.org/packages/f6/39/8c30ca4d2fd8e69b942f8151b1bdb67aeafd6dfa208c7f1a1e5f6c903287/sequana_depletion-0.3.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-12-17 09:17:42",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "sequana",
"github_project": "depletion",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"lcname": "sequana-depletion"
}
JSON
