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https://github.com/sequana/fastqc
sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
https://github.com/sequana/fastqc
fastqc ngs sequana snakemake
Last synced: about 2 months ago
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sequana pipeline to perform parallel fastqc and summarize results with multiqc plot
- Host: GitHub
- URL: https://github.com/sequana/fastqc
- Owner: sequana
- License: bsd-3-clause
- Created: 2019-11-22T21:45:07.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2024-10-31T21:00:34.000Z (2 months ago)
- Last Synced: 2024-10-31T21:29:30.707Z (2 months ago)
- Topics: fastqc, ngs, sequana, snakemake
- Language: Python
- Homepage:
- Size: 1.48 MB
- Stars: 3
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
.. image:: https://badge.fury.io/py/sequana-fastqc.svg
:target: https://pypi.python.org/pypi/sequana_fastqc
.. 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/fastqc/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/fastqc/actions/workflows/main.yml
.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
:target: https://pypi.python.org/pypi/sequana
:alt: Python 3.8 | 3.9 | 3.10
This is is the **fastqc** pipeline from the `Sequana `_ projet
:Overview: Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
:Input: A set of FastQ files (paired or single-end) compressed or not
:Output: An HTML file summary.html (individual fastqc reports, mutli-samples report)
:Status: Production
:Wiki: https://github.com/sequana/fastqc/wiki
:Documentation: This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io
:Citation: Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352
Installation
~~~~~~~~~~~~
sequana_fastqc is based on Python3, just install the package as follows::
pip install sequana_fastqc --upgrade
You will need third-party software such as fastqc. Please see below for details.
Usage
~~~~~
If you have a set of FastQ files in a data/ directory, type::
sequana_fastqc --input-directory data
To know more about the options (e.g., add a different pattern to restrict the
execution to a subset of the input files, change the output/working directory,
etc)::
sequana_fastqc --help
The call to sequana_fastqc creates a directory **fastqc**. Then, you go to the
working directory and execute the pipeline as follows::
cd fastqc
sh fastqc.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters::
snakemake -s fastqc.rules --cores 4 --stats stats.txt
Or use `sequanix `_ interface.
Please see the `Wiki `_ for more examples and features.
Tutorial
~~~~~~~~
You can retrieve test data from sequana_fastqc (https://github.com/sequana/fastqc) or type::
wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz
wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gz
then, prepare the pipeline::
sequana_fastqc --input-directory .
cd fastqc
sh fastq.sh
# once done, remove temporary files (snakemake and others)
make clean
Just open the HTML entry called summary.html. A multiqc report is also available.
You will get expected images such as the following one:
.. image:: https://github.com/sequana/fastqc/blob/main/doc/summary.png?raw=true
Please see the `Wiki `_ for more examples and features.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- fastqc
- falco (optional)
For Linux users, we provide apptainer/singularity images available through the **damona** project (https://damona.readthedocs.io).
To make use of them, initiliase the pipeline with the --use-apptainer option and everything should be downloaded
automatically for you, which also guarantees reproducibility::
sequana_fastqc --input-directory data --use-apptainer --apptainer-prefix ~/images
.. image:: https://raw.githubusercontent.com/sequana/fastqc/main/sequana_pipelines/fastqc/dag.png
Details
~~~~~~~~~
This pipeline runs fastqc in parallel on the input fastq files (paired or not)
and then execute multiqc. A brief sequana summary report is also produced.
s
You may use falco instead of fastqc. This is experimental but seem to work for
Illumina/FastQ files.
This pipeline has been tested on several hundreds of MiSeq, NextSeq, MiniSeq,
ISeq100, Pacbio runs.
It produces a md5sum of your data. It copes with empty samples. Produces
ready-to-use HTML reports, etc
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
========= ====================================================================
1.8.2 * Fix the onerror typo in the pipeline, fix CI.
1.8.1 * update __init__ (version)
1.8.0 * uses pyproject instead of setuptools
* uses click instead of argparse and newest sequana_pipetools
(0.16.0)
1.7.1 * Set wrapper version in the config based on new sequana_pipetools
feature
1.7.0 * Use new rulegraph wrapper and new graphviz apptainer
1.6.2 * slight refactorisation to use rulegraph wrapper
1.6.1 * pin sequana version to 1.4.4 to force usage of new fastqc module
to fix falco. Updated config documentation.
1.6.0 * Fixed falco output error and use singularity containers
1.5.0 * removed modules completely.
1.4.2 * simplified pipeline (suppress setup and use existing wrapper)
1.4.1 * simplified pipeline with wrappers/rules
1.4.0 * This version uses sequana 0.12.0 and new sequana-wrappers
mechanism. Functionalities is unchanged. Also based on
sequana_pipetools 0.6.X
1.3.0 * add option --skip-multiqc (in case of memory trouble)
* Fix typo in the link towards fastqc reports in the summary.html
table
* Fix number of samples in the paired case (divide by 2)
1.2.0 * compatibility with Sequanix
* Fix pipeline to cope with new snakemake API
1.1.0 * add new rule to allow users to choose falco software instead of
fastqc. Note that fastqc is 4 times faster but still a work in
progress (version 0.1 as of Nov 2020).
* allows the pipeline to process pacbio files (in fact any files
accepted by fastqc i.e. SAM and BAM files
* More doc, test and info on the wiki
1.0.1 * add md5sum of input files as md5.txt file
1.0.0 * a stable version. Added a wiki on github as well and a
singularity recipes
0.9.15 * For the HTML reports, takes into account samples with zero reads
0.9.14 * round up some statistics in the main table
0.9.13 * improve the summary HTML report
0.9.12 * implemented new --from-project option
0.9.11 * now depends on sequana_pipetools instead of sequana.pipelines to
speed up --help calls
* new summary.html report created with pipeline summary
* new rule (plotting)
0.9.10 * simplify the onsuccess section
0.9.9 * add missing png and pipeline (regression bug)
0.9.8 * add missing multi_config file
0.9.7 * check existence of input directory in main.py
* add a logo
* fix schema
* add multiqc_config
* add sequana + sequana_fastqc version
0.9.6 add the readtag option
========= ====================================================================
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.