https://github.com/sequana/sequana_merge_flowcells
merge 2 or more flowcells (with identical design) into a single set of FastQ files
https://github.com/sequana/sequana_merge_flowcells
Last synced: about 1 year ago
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merge 2 or more flowcells (with identical design) into a single set of FastQ files
- Host: GitHub
- URL: https://github.com/sequana/sequana_merge_flowcells
- Owner: sequana
- License: bsd-3-clause
- Created: 2020-11-17T11:30:20.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-11-17T12:11:32.000Z (over 5 years ago)
- Last Synced: 2024-12-25T02:42:14.678Z (over 1 year ago)
- Language: Python
- Size: 58.6 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
This is is the **merge_flowcells** pipeline from the `Sequana `_ project
:Overview: Merge gzipped FastQ files from several flowcells
:Input: set of identically named FastQ files from several directories
:Output: merged FastQ files stored in an output directory.
:Status: mature
: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_merge_flowcells
Usage
~~~~~
::
sequana_pipelines_merge_flowcells --help
sequana_pipelines_merge_flowcells --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::
cd merge_flowcells
sh merge_flowcells.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 merge_flowcells.rules -c config.yaml --cores 4 --stats stats.txt
Or use `sequanix `_ interface.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- sequana
- pigz
- zcat
.. image:: https://raw.githubusercontent.com/sequana/sequana_merge_flowcells/master/sequana_pipelines/merge_flowcells/dag.png
Details
~~~~~~~~~
This pipeline runs **merge_flowcells** in parallel on the input fastq files (paired or not).
You have to provide at least two subdirectories. You may provide more.
The input FastQ files must be zipped in the current version. The input FastQ
files found in the first directory muts be found in all subsequent directories.
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
~~~~~~~~~
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Version Description
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0.0.1 **First release.**
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