update feature-benchmark branch (#158)

* adding viloca to the workflow

* fix file paths

* update conig_schema

* adding paired_end_read_merger

* update rule for paired_en_read_merger + add conda env definition

* update rule for paired_en_read_merger + add conda env definition

* update enviroment

* add paired_end_read_merger

* update paired_end_read_merger rule

* add conda package to env

* Viloca touch ups

- snakemake handles `directory()`
- VILOCA 1.0.0 on bioconda
- use GitLab for smallgenomeutilites due to GitHub LFS limitations

* Linting

* Generate copnfig manual

* Documentation touch ups

- update paper: V-pipe 3.0 pre-print
- WorkflowHub's required documentation.md points to our documentation
- Update Tutorial intro page: point to installer

* improve tutorial_0_install.md

* Links to bioconda in installation tutorial

* Singularity+conda support

* Update README.md  with viloca reference

* Add issue templates

* Contributing guidelines

* Disable linter for templates

* bugfix: viloca

- typo fix
- all: depends on correct CSV

* bugfix: bump versions of bcftools and cyvcf2

- recent change of numpy in bioconda breaks older cyvcf

* [bump] LolliPop 0.4.0

- support new `filters` option

* Update of conf manual

* [bump] LolliPop v0.4.1

---------

Co-authored-by: Ivan Blagoev Topolsky <[email protected]>
Co-authored-by: Prajwal Kulkarni <[email protected]>
Co-authored-by: Ivan Blagoev Topolsky <[email protected]>

.github/ISSUE_TEMPLATE/01_report_bug.md

@@ -0,0 +1,28 @@
+---
+name: 🐛 Report a bug
+about: Tell us if something is broken or needs attention
+labels: t:bug, help wanted, good first issue, needs triage
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior, e.g.:
+1. V-pipe configuration file used '...'
+2. Samples TSV file used '....'
+3. Commands executed '.vpipe --core 4 ...'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Linux, Mac OS]
+ - Version [e.g. v3.0.0, master branch]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/02_request_feature.md

@@ -0,0 +1,17 @@
+---
+name: 🙋 Request a feature
+about: Suggest an improvement, tell about your idea 
+labels: t:feat, help wanted, good first issue, needs triage
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when ...
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/03_ask.md

@@ -0,0 +1,5 @@
+---
+name: ❓ Ask
+about: Ask a question about this project
+labels: t:ask, needs triage
+---

.github/ISSUE_TEMPLATE/04_discuss.md

@@ -0,0 +1,5 @@
+---
+name: 💬 Discuss
+about: Talk to the team
+labels: t:talk, needs triage
+---

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.mega-linter.yml

@@ -20,3 +20,5 @@ SHOW_ELAPSED_TIME: true
 DEFAULT_BRANCH: master
 # any further fix to LICENSE.md will break licensee's detection scheme
 MARKDOWN_MARKDOWNLINT_FILTER_REGEX_EXCLUDE: LICENSE\.md
+# GitHub passes HTML comments verbatime from template so we can't use <!-- markdownlint-disable MD041 -->
+FILTER_REGEX_EXCLUDE: (\.github/ISSUE_TEMPLATE/.*\.md)

.snakemake-workflow-catalog.yml

@@ -2,5 +2,5 @@ usage:
   software-stack-deployment:
     conda: true
     singularity: false
-    singularity+conda: false
+    singularity+conda: true
   report: false

CONTRIBUTING.md

@@ -0,0 +1,57 @@
+
+# Contributing to V-pipe
+
+A big welcome and thank you for considering contributing to V-pipe! It’s people like you that make it a reality for users in our community.
+
+Reading and following these guidelines will help us make the contribution process easy and effective for everyone involved. It also communicates that you agree to respect the time of the developers managing and developing these open source projects. In return, we will reciprocate that respect by addressing your issue, assessing changes, and helping you finalize your pull requests.
+
+## Quicklinks
+
+* [Getting Started](#getting-started)
+    * [Issues](#issues)
+    * [Pull Requests](#pull-requests)
+* [Getting Help](#getting-help)
+
+## Getting Started
+
+Contributions are made to this repo via Issues and Pull Requests (PRs). A few general guidelines that cover both:
+
+- Search for existing Issues and PRs before creating your own.
+- We work hard to makes sure issues are handled in a timely manner but, depending on the impact, it could take a while to investigate the root cause. A friendly ping in the comment thread to the submitter or a contributor can help draw attention if your issue is blocking.
+
+### Issues
+
+Issues should be used to report problems with the V-pipe workflow, request a new feature, or to discuss potential changes before a PR is created. When you create a new Issue, a template will be loaded that will guide you through collecting and providing the information we need to investigate.
+
+If you find an Issue that addresses the problem you're having, please add your own reproduction information to the existing issue rather than creating a new one. Adding a [reaction](https://github.blog/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/) can also help be indicating to our maintainers that a particular problem is affecting more than just the reporter.
+
+### Pull Requests
+
+PRs to our workflow are always welcome and can be a quick way to get your fix or improvement slated for the next release. In general, PRs should:
+
+- Target our staging branch: [rubicon](https://github.com/cbg-ethz/V-pipe/tree/rubicon)
+- Only fix/add the functionality in question **OR** address wide-spread whitespace/style issues, not both.
+- Add unit or integration tests for fixed or changed functionality (if a test suite already exists).
+  - Or at least provide a minimalist example dataset
+- Address a single concern in the least number of changed lines as possible.
+- Include documentation in the repo or on our `docs/` directory.
+
+For changes that address core functionality or would require breaking changes (e.g. a major release), it's best to open an Issue to discuss your proposal first. This is not required but can save time creating and reviewing changes.
+
+In general, we follow the ["fork-and-pull" Git workflow](https://github.com/susam/gitpr)
+
+1. Fork the repository to your own Github account
+2. Clone the project to your machine
+3. Create a branch locally with a succinct but descriptive name
+4. Commit changes to the branch
+5. Following any formatting and testing guidelines specific to this repo
+   - We rely on [snakefmt](https://github.com/snakemake/snakefmt) for Snakemake files
+   - We use [Mega-Linter](https://megalinter.io) for the remaining files (Python (Black), Jupyter (Jupyfmt), Markdown (Markdownlint), Bash (Shellcheck), Perl (Perlcritic), Docker (Hadolint))
+   - Ask us for help if you have trouble linting your code
+6. Push changes to your fork
+7. Open a PR in our repository and follow the PR template so that we can efficiently review the changes.
+
+## Getting Help
+
+Join us in the [V-pipe Gitter channel](https://gitter.im/V-pipe/community) (also [accessible over matrix](https://matrix.to/#/#V-pipe_community:gitter.im?utm_source=gitter) from your favorite client) and post your question there to reach out the devs.
+For further inquiries, you can also contact the V-pipe Dev Team by opening a ticket at [[email protected]](mailto:[email protected]).

README.md

@@ -162,9 +162,9 @@ Other dependencies are managed by using isolated conda environments per rule, an
 
 If you use this software in your research, please cite:
 
-Posada-Céspedes S., Seifert D., Topolsky I., Jablonski K.P., Metzner K.J., and Beerenwinkel N. 2021.
-"V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data."
-_Bioinformatics_, January. doi:[10.1093/bioinformatics/btab015](https://doi.org/10.1093/bioinformatics/btab015).
+Fuhrmann, L., Jablonski, K. P., Topolsky, I., Batavia, A. A., Borgsmueller, N., Icer Baykal, P., Carrara, M. ... & Beerenwinkel, (2023).
+"V-Pipe 3.0: A Sustainable Pipeline for Within-Sample Viral Genetic Diversity Estimation."
+_bioRxiv_, doi:[10.1101/2023.10.16.562462](https://doi.org/10.1101/2023.10.16.562462).
 
 ## Contributions