Merge pull request #3 from Clinical-Virology-Unit/merge-daan-v0.0.6-to-v0.0.9

Merge daan v0.0.6 to v0.0.9

Author: DaanJansen94

.gitignore

@@ -1,8 +1,22 @@
-# Nextflow runtime / temporary artifacts (repo root)
+Databases/
+Databases1/
+host/
+
+## Nextflow run artefacts
 .nextflow/
 .nextflow.log*
 work/
+trace*
+timeline*
+report*
+dag*
 
-# Local pulled databases (large, reproducible)
-Databases/
+## Common OS / editor noise
+.DS_Store
+Thumbs.db
+
+## Python packaging artefacts
+*.egg-info/
 
+## Nextflow config evaluation artefacts (should not be created)
+_nf_config_*

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+authors:
+  - family-names: Jansen
+    given-names: Daan
+    orcid: https://orcid.org/0000-0003-4612-6891
+  - family-names: De Souza Novaes
+    given-names: Ane
+    orcid: https://orcid.org/0000-0003-3089-2102
+  - family-names: de Block
+    given-names: Tessa
+    orcid: https://orcid.org/0000-0003-3294-0147
+  - family-names: Rezende
+    given-names: Antonio Mauro
+    orcid: https://orcid.org/0000-0003-4775-1779
+  - family-names: Vercauteren
+    given-names: Koen
+    orcid: https://orcid.org/0000-0003-1472-9938
+
+title: "Metatropics: Human viral pathogen identification and consensus genome calling from nanopore metagenomic sequencing data."
+abstract: >-
+  Metatropics is a Nextflow pipeline for Oxford Nanopore metagenomic reads, focused on detecting human viral pathogens
+  and creating viral consensus genomes. Workflows start from raw POD5 (with optional GPU basecalling) or pre-basecalled
+  FASTQ, then proceed with read quality control, alignment, host depletion, and taxonomic profiling, followed by
+  consensus genome building—polishing, refinement, and consensus calling. One container image per process keeps
+  runs portable and reproducible under Docker, Singularity/Apptainer, and typical HPC setups.
+version: 0.0.9
+date-released: 2026-03-31
+url: https://github.com/DaanJansen94/Metatropics
+repository-code: https://github.com/DaanJansen94/Metatropics
+license: MIT

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible 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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

Databases/.gitattributes

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Antonio Mauro Rezende
+Copyright (c) 2026 Metatropics contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal