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update first true release
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‎LICENSE

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BSD 3-Clause License
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Copyright (c) 2016-2019, Sequana Development Team
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.rst

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This is is the **bioconvert** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
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:Overview: TODO
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:Input: TODO
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:Output: TODO
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:Status: draft
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: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
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Installation
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~~~~~~~~~~~~
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You must install Sequana first::
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pip install sequana
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Then, just install this package::
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pip install sequana_bioconvert
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Usage
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~~~~~
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::
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sequana_pipelines_bioconvert --help
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You need to provide the type of conversion you wish to perform with the
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*--command* argument. You also need to tell the type of extensions expected
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including the compression (gz, bz2 or dsrc recognised). Finally, the
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*--input-directory* and *--input-pattern* must be used to find the input
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files.::
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sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext
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fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"
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This creates a directory with the pipeline and configuration file. You will then need
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to execute the pipeline::
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cd bioconvert
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sh bioconvert.sh # for a local run
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This launch a snakemake pipeline. Symboli links to the input data are created in
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the ./input directory and results stored in the ./output directory.
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See bioconvert.readthedocs.io for more details about **bioconvert** itself.
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If you are familiar with snakemake, you can retrieve the pipeline itself and its
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configuration files and then execute the pipeline yourself with specific parameters::
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snakemake -s bioconvert.rules -c config.yaml --cores 4 --stats stats.txt
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Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
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Requirements
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~~~~~~~~~~~~
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This pipelines requires the following executable(s):
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- bioconvert
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.. image:: https://raw.githubusercontent.com/sequana/sequana_bioconvert/master/sequana_pipelines/bioconvert/dag.png
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Details
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~~~~~~~~~
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This pipeline runs **bioconvert** in parallel on the input fastq files (paired or not).
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A brief sequana summary report is also produced.
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Rules and configuration details
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_bioconvert/master/sequana_pipelines/bioconvert/config.yaml>`_
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to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
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Changelog
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~~~~~~~~~
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========= ====================================================================
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Version Description
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========= ====================================================================
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0.8.1 **Working version**
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0.8.0 **First release.**
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========= ====================================================================
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‎doc/Makefile

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# Makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS =
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SPHINXBUILD = sphinx-build
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PAPER =
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BUILDDIR = build
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# Internal variables.
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PAPEROPT_a4 = -D latex_paper_size=a4
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PAPEROPT_letter = -D latex_paper_size=letter
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ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
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.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
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help:
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@echo "Please use \`make <target>' where <target> is one of"
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@echo " html to make standalone HTML files"
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@echo " dirhtml to make HTML files named index.html in directories"
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@echo " singlehtml to make a single large HTML file"
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@echo " pickle to make pickle files"
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@echo " json to make JSON files"
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@echo " htmlhelp to make HTML files and a HTML help project"
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@echo " qthelp to make HTML files and a qthelp project"
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@echo " devhelp to make HTML files and a Devhelp project"
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@echo " epub to make an epub"
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@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
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@echo " latexpdf to make LaTeX files and run them through pdflatex"
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@echo " text to make text files"
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@echo " man to make manual pages"
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@echo " changes to make an overview of all changed/added/deprecated items"
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@echo " linkcheck to check all external links for integrity"
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@echo " doctest to run all doctests embedded in the documentation (if enabled)"
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clean:
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-rm -rf $(BUILDDIR)/*
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html:
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$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
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dirhtml:
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$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
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@echo
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@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
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singlehtml:
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$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
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@echo
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@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
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pickle:
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$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
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@echo
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@echo "Build finished; now you can process the pickle files."
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json:
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$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
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@echo
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@echo "Build finished; now you can process the JSON files."
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htmlhelp:
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$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
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@echo
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@echo "Build finished; now you can run HTML Help Workshop with the" \
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".hhp project file in $(BUILDDIR)/htmlhelp."
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qthelp:
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$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
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@echo
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@echo "Build finished; now you can run "qcollectiongenerator" with the" \
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".qhcp project file in $(BUILDDIR)/qthelp, like this:"
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@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/ebisoftware.qhcp"
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@echo "To view the help file:"
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@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/ebisoftware.qhc"
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devhelp:
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$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
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@echo
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@echo "Build finished."
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@echo "To view the help file:"
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@echo "# mkdir -p $$HOME/.local/share/devhelp/ebisoftware"
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@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ebisoftware"
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@echo "# devhelp"
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epub:
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$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
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@echo
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@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
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latex:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo
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@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
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@echo "Run \`make' in that directory to run these through (pdf)latex" \
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"(use \`make latexpdf' here to do that automatically)."
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latexpdf:
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$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
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@echo "Running LaTeX files through pdflatex..."
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make -C $(BUILDDIR)/latex all-pdf
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@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
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text:
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$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
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@echo
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@echo "Build finished. The text files are in $(BUILDDIR)/text."
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man:
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$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
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@echo
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@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
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changes:
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$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
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@echo
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@echo "The overview file is in $(BUILDDIR)/changes."
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linkcheck:
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$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
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@echo
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@echo "Link check complete; look for any errors in the above output " \
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"or in $(BUILDDIR)/linkcheck/output.txt."
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doctest:
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$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
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@echo "Testing of doctests in the sources finished, look at the " \
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"results in $(BUILDDIR)/doctest/output.txt."
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