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Merge FastQ from different projects (flowcells) into single project

Project description

This is is the merge_flowcells pipeline from the Sequana project


Merge gzipped FastQ files from several flowcells


set of identically named FastQ files from several directories


merged FastQ files stored in an output directory.




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


You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_merge_flowcells


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  # 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.


This pipelines requires the following executable(s):

  • sequana

  • pigz

  • zcat


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.





First release.

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Source Distribution

sequana_merge_flowcells-0.9.3.tar.gz (6.2 kB view hashes)

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