:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'illumina-cleanup' .. highlight: bash illumina-cleanup ================ .. conda:recipe:: illumina-cleanup :replaces_section_title: :noindex: Nextflow pipeline for pre\-processing Illumina FASTQ files :homepage: https://github.com/rpetit3/illumina-cleanup :license: MIT :recipe: /`illumina-cleanup `_/`meta.yaml `_ .. conda:package:: illumina-cleanup |downloads_illumina-cleanup| |docker_illumina-cleanup| :versions: ``1.0.0-2``,  ``1.0.0-1``,  ``1.0.0-0`` :depends bbmap: :depends fastq-scan: :depends fastqc: :depends lighter: :depends nextflow: :depends pigz: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install illumina-cleanup and update with:: mamba update illumina-cleanup To create a new environment, run:: mamba create --name myenvname illumina-cleanup with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/illumina-cleanup: (see `illumina-cleanup/tags`_ for valid values for ````) .. |downloads_illumina-cleanup| image:: https://img.shields.io/conda/dn/bioconda/illumina-cleanup.svg?style=flat :target: https://anaconda.org/bioconda/illumina-cleanup :alt: (downloads) .. |docker_illumina-cleanup| image:: https://quay.io/repository/biocontainers/illumina-cleanup/status :target: https://quay.io/repository/biocontainers/illumina-cleanup .. _`illumina-cleanup/tags`: https://quay.io/repository/biocontainers/illumina-cleanup?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/illumina-cleanup/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/illumina-cleanup/README.html