Merge pull request #1 from biowdl/BIOWDL-328

Convert samplesheets directly into BioWDL processable format

.github/PULL_REQUEST_TEMPLATE.md

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+
+### Checklist
+- [ ] Pull request details were added to CHANGELOG.rst

.github/release_checklist.md

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+Release checklist
+- [ ] Check outstanding issues on JIRA and Github
+- [ ] Check [latest documentation
+](https://biowdl-input-converter.readthedocs.io/en/latest/) looks fine
+- [ ] Create a release branch 
+  - [ ] Set version to a stable number.
+  - [ ] Change current development version in `CHANGELOG.rst` to stable version.
+- [ ] Merge the release branch into `master`
+- [ ] Create a test pypi package from the master branch. ([Instructions.](
+https://packaging.python.org/tutorials/packaging-projects/#generating-distribution-archives
+))
+- [ ] Install the packages from the test pypi repository to see if they work.
+- [ ] Created an annotated tag with the stable version number. Include changes 
+from `CHANGELOG.rst`.
+- [ ] Push tag to remote.
+- [ ] Push tested packages to pypi
+- [ ] merge `master` branch back into `develop`.
+- [ ] Add updated version number to develop
+- [ ] Update the package on bioconda
+- [ ] Build the new tag on readthedocs. Only build the last patch version of
+each minor version. So `1.1.1` and `1.2.0` but not `1.1.0`, `1.1.1` and `1.2.0`.

.gitignore

@@ -1 +1,104 @@
-__pycache__
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

.travis.yml

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+language: python
+install:
+  - pip install tox
+dist: xenial
+python: 3.7  # Use the oldest supported version of python as default.
+script:
+    - tox -e $TOX_ENV
+matrix:
+  include:
+    - env: TOX_ENV=lint
+    - env: TOX_ENV=docs
+    - env: TOX_ENV=py37
+      install:
+        - pip install codecov
+        - pip install tox
+      after_success:
+        # Correct coverage xml for coverage services.
+        - >
+          bash -c 'set -eux;
+          pkg_path=$(find .tox/py*/lib/python*/site-packages/biowdl_input_converter -maxdepth 0 -type d);
+          sed -i "s:${pkg_path}:src/biowdl_input_converter:g" coverage.xml'
+        - codecov -v  # -v to make sure coverage upload works.
+

CHANGELOG.rst

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+==========
+Changelog
+==========
+
+.. Newest changes should be on top.
+
+.. NOTE: This document is user facing. Please word the changes in such a way
+.. that users understand how the changes affect the new version.
+
+0.1.0-dev
+---------------
++ Added documentation and readthedocs page
++ Added changelog and release procedures
++ Added test suite with coverage metrics, enabled CI
++ Add validate flag to allow users to validate files
++ Added command line interface with ability to write to stdout and files
++ Added ability to check files for presence and md5sum checking
++ Added sample group -> old style JSON/YAML conversion
++ Added sample group -> new style JSON/YAML conversion
++ Added yaml -> sample group conversion
++ Reworked csv conversion by @DavyCats to fit the new sample group structure
++ Added sample group structure to enable any-to-any conversions

LICENSE

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+MIT License
+
+Copyright (c) 2019 Leiden University Medical Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

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+.. Badges have empty alts. So nothing shows up if they do not work.
+
+.. image:: https://img.shields.io/pypi/v/biowdl-input-converter.svg
+  :target: https://pypi.org/project/biowdl-input-converter/
+  :alt:
+
+.. image:: https://img.shields.io/conda/v/bioconda/biowdl-input-converter.svg
+  :target: http://bioconda.github.io/recipes/biowdl-input-converter/README.html
+  :alt:
+
+.. image:: https://img.shields.io/pypi/pyversions/biowdl-input-converter.svg
+  :target: https://pypi.org/project/biowdl-input-converter/
+  :alt:
+
+.. image:: https://img.shields.io/pypi/l/biowdl-input-converter.svg
+  :target: https://github.com/biowdl/biowdl-input-converter/blob/master/LICENSE
+  :alt:
+
+.. image:: https://travis-ci.org/biowdl/biowdl-input-converter.svg?branch=develop
+  :target: https://travis-ci.org/biowdl/biowdl-input-converter
+  :alt:
+
+.. image:: https://codecov.io/gh/biowdl/biowdl-input-converter/branch/develop/graph/badge.svg
+  :target: https://codecov.io/gh/biowdl/biowdl-input-converter
+  :alt:
+
+========================
+BioWDL input converter
+========================
+
+biowdl-input-converter converts human-readable samplesheets into
+a format that can be easily processed by BioWDL pipelines.
+
+Check out the documentation on https://biowdl-input-converter.readthedocs.io
+for more information on installation and usage.
+
+For more information on BioWDL check out the documentation on
+https://biowdl.github.io.

codecov.yml

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+comment: off
+coverage:
+  status:
+    project:
+      default:
+        target: 90  # let's try to hit high standards
+    patch:
+      default:
+        target: 90  # Tests should be written for new features

docs/CHANGELOG.rst

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+../CHANGELOG.rst

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+from distutils.dist import DistributionMetadata
+from pathlib import Path
+
+import pkg_resources
+
+# Get package information from the installed package.
+package = pkg_resources.get_distribution("biowdl_input_converter")
+metadata_file = Path(package.egg_info) / Path(package.PKG_INFO)
+metadata = DistributionMetadata(path=str(metadata_file))
+
+project = metadata.name
+copyright = '2019, Leiden University Medical Center'
+author = metadata.author
+
+# The short X.Y version
+version = package.parsed_version.base_version
+# The full version, including alpha/beta/rc tags
+release = package.version
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinxarg.ext'
+]
+
+# The master toctree document.
+master_doc = 'index'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+html_theme_options = dict(
+    display_version=True,
+)
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']

docs/csv_examples/example.csv

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+"sample","library","readgroup","R1","R1_md5","R2","R2_md5","HiSeq4000","other_property"
+"s1","lib1","rg1","r1_1.fq","181a657e3f9c3cde2d3bb14ee7e894a3","r1_2.fq",,"yes","pizza"
+"s2","lib1","rg1","r2_1.fq",,"r2_2.fq",dc2776dc3a07c4f468455bae1a8ff872,"no",