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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/nanomerge/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/nanomerge/actions/workflows\n\n.. image:: https://coveralls.io/repos/github/sequana/nanomerge/badge.svg?branch=main\n   :target: https://coveralls.io/github/sequana/nanomerge?branch=main\n\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://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg\n    :target: https://pypi.python.org/pypi/sequana\n    :alt: Python 3.8 | 3.9 | 3.10\n\n\n\n\nThis is is the **nanomerge** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: merge fastq files generated by Nanopore run and generates raw data QC.\n:Input: individual fastq files generated by nanopore demultiplexing\n:Output: merged fastq files for each barcode (or unique sample)\n:Status: production\n: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\n\n\nInstallation\n~~~~~~~~~~~~\n\nYou can install the packages using pip::\n\n    pip install sequana_nanomerge --upgrade\n\nAn optional requirements is pycoQC, which can be install with conda/mamba using e.g.::\n\n    conda install pycoQC\n\nyou will also need graphviz installed.\n\nUsage\n~~~~~\n\n::\n\n    sequana_nanomerge --help\n\nIf you data is barcoded, they are usually in sub-directories barcoded/barcodeXY so you will need to use a pattern\n(--input-pattern) such as `*/*.gz`::\n\n    sequana_nanomerge --input-directory DATAPATH/barcoded --samplesheet samplesheet.csv\n        --summary summary.txt --input-pattern '*/*fastq.gz'\n\notherwise all fastq files are in DATAPATH/ so the input pattern can just be `*.fastq.gz`::\n\n    sequana_nanomerge --input-directory DATAPATH --samplesheet samplesheet.csv\n        --summary summary.txt --input-pattern '*fastq.gz'\n\nThe --summary is optional and takes as input the output of albacore/guppy demultiplexing. usually a file called sequencing_summary.txt\n\nNote that the different between the two is the extra `*/` before the `*.fastq.gz` pattern since barcoded files are in individual subdirectories.\n\nIn both bases, the command creates a directory with the pipeline and configuration file. You will then need to execute the pipeline::\n\n    cd nanomerge\n    sh nanomerge.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 nanomerge.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/master/sequanix.html\u003e`_ interface.\n\nConcerning the sample sheet, whether your data is barcoded or not, it should be a CSV file ::\n\n    barcode,project,sample\n    barcode01,main,A\n    barcode02,main,B\n    barcode03,main,C\n\nFor a non-barcoded run, you must provide a file where the barcode column can be set (empty)::\n\n    barcode,project,sample\n    ,main,A\n\nor just removed::\n\n    project,sample\n    main,A\n\nUsage with apptainer:\n~~~~~~~~~~~~~~~~~~~~~~~~~\n\nWith apptainer, initiate the working directory as follows::\n\n    sequana_nanomerge --use-apptainer\n\nImages are downloaded in the working directory but you can store then in a directory globally (e.g.)::\n\n    sequana_nanomerge --use-apptainer --apptainer-prefix ~/.sequana/apptainers\n\nand then::\n\n    cd nanomerge\n    sh nanomerge.sh\n\nif you decide to use snakemake manually, do not forget to add apptainer options::\n\n    snakemake -s nanomerge.rules -c config.yaml --cores 4 --stats stats.txt --use-apptainer --apptainer-prefix ~/.sequana/apptainers --apptainer-args \"-B /home:/home\"\n\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s), which is optional:\n\n- pycoQC\n- dot\n\n.. image:: https://raw.githubusercontent.com/sequana/nanomerge/main/sequana_pipelines/nanomerge/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **nanomerge** 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 \u003chttps://raw.githubusercontent.com/sequana/sequana_nanomerge/master/sequana_pipelines/nanomerge/config.yaml\u003e`_\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========= ====================================================================\n1.5.1     * Fix wrappers tag\n1.5.0     * refactoring to use Click\n1.4.0     * sub sampling was biased in v1.3.0. Using stratified sampling to \n            correcly sample large file. Also set a --promethion option that\n            auomatically sub sample 10% of the data\n          * add summary table\n1.3.0     * handle large promethium run by using a sub sample of the \n            sequencing summary file (--sample of pycoQC still loads the entire\n            file in memory)\n1.2.0     * handle large promethium run by using find+cat instead of just \n            cat to cope with very large number of input files.\n1.1.0     * add subsample option and set to 1,000,000 reads to handle large \n            runs such as promethion\n1.0.1     * CSV can now handle sample or samplename column name in samplesheet.\n          * Fix the pyco file paths, update requirements and doc\n1.0.0     Stable release ready for production\n0.0.1     **First release.**\n========= ====================================================================\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fnanomerge","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fnanomerge","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fnanomerge/lists"}