diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 00000000..45cb1077 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, body +size, disability, ethnicity, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, nationality, personal +appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or + advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an appointed +representative at an online or offline event. Representation of a project may be +further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at odiogosilva@gmail.com. All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and appropriate to the circumstances. The project team is +obligated to maintain confidentiality with regard to the reporter of an incident. +Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq diff --git a/README.md b/README.md index 5273a198..9ddffcce 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ [![Documentation Status](https://readthedocs.org/projects/flowcraft/badge/?version=latest)](http://flowcraft.readthedocs.io/en/latest/?badge=latest) [![PyPI version](https://badge.fury.io/py/flowcraft.svg)](https://badge.fury.io/py/flowcraft) [![Anaconda-Server Badge](https://anaconda.org/bioconda/flowcraft/badges/version.svg)](https://anaconda.org/bioconda/flowcraft) +[![Gitter](https://badges.gitter.im/flowcraft-community/community.svg)](https://gitter.im/flowcraft-community/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)

nextflow_logo diff --git a/docs/user/components/spades.rst b/docs/user/components/spades.rst index b27f6bda..3defb87b 100644 --- a/docs/user/components/spades.rst +++ b/docs/user/components/spades.rst @@ -47,7 +47,7 @@ Default directives - ``cpus``: 4 - ``memory``: 5GB (dynamically increased on retry) - ``container``: ummidock/spades -- ``version``: 3.11.1-1 +- ``version``: 3.13.0-1 - ``scratch``: true Advanced @@ -56,4 +56,4 @@ Advanced Template ^^^^^^^^ -:mod:`flowcraft.templates.spades` \ No newline at end of file +:mod:`flowcraft.templates.spades` diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py index 69a5d5ff..8b0e62ef 100755 --- a/flowcraft/flowcraft.py +++ b/flowcraft/flowcraft.py @@ -7,8 +7,6 @@ import argparse import logging.config -from distutils.dir_util import copy_tree - from os.path import join, dirname try: @@ -268,16 +266,16 @@ def copy_project(path): target_dir = dirname(path) # Copy templates - copy_tree(join(repo_dir, "templates"), join(target_dir, "templates")) + shutil.copytree(join(repo_dir, "templates"), join(target_dir, "templates"), dirs_exist_ok=True) # Copy Helper scripts - copy_tree(join(repo_dir, "lib"), join(target_dir, "lib")) + shutil.copytree(join(repo_dir, "lib"), join(target_dir, "lib"), dirs_exist_ok=True) # Copy resources dir - copy_tree(join(repo_dir, "resources"), join(target_dir, "resources")) + shutil.copytree(join(repo_dir, "resources"), join(target_dir, "resources"), dirs_exist_ok=True) # Copy bin scripts - copy_tree(join(repo_dir, "bin"), join(target_dir, "bin")) + shutil.copytree(join(repo_dir, "bin"), join(target_dir, "bin"), dirs_exist_ok=True) # Copy static profiles file shutil.copy(join(repo_dir, "profiles.config"),