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
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
Version |
Description |
|---|---|
0.0.1 |
First release. |
1 maintainer
Release files for sequana-merge-flowcells 0.9.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sequana_merge_flowcells-0.9.3.tar.gz | 6.2 kB | Details |
Release files / sequana_merge_flowcells-0.9.3.tar.gz
| Download URL | sequana_merge_flowcells-0.9.3.tar.gz |
|---|---|
| Size | 6.2 kB |
| Tags | Source |
|
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07b12495b89de14ece330f48667ca7f2b823dbb195e20eaa616bd4834c49292b
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twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/49.6.0.post20200917 requests-toolbelt/0.9.1 tqdm/4.50.0 CPython/3.7.3
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