remove nf-core branding per https://nf-co.re/docs/contributing/tutori…

…als/unofficial_pipelines#removing-nf-core-only-branding

.github/CONTRIBUTING.md

@@ -9,16 +9,12 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/tada then the best place to ask is on the nf-core Slack [#tada](https://nfcore.slack.com/channels/tada) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
-
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/tada, the standard workflow is as follows:
+If you'd like to write some code for TADA, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/tada issues](https://github.com/nf-core/tada/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/tada repository](https://github.com/nf-core/tada) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-core/tada issues](https://github.com/h3abionet/TADA/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/tada repository](https://github.com/h3abionet/TADA) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -59,7 +55,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/tada documentation](https://nf-co.re/tada/usage) and don't hesitate to get in touch on the nf-core Slack [#tada](https://nfcore.slack.com/channels/tada) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [TADA documentation](https://github.com/h3abionet/TADA/usage).
 
 ## Pipeline contribution conventions
 
@@ -106,18 +102,3 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-
-## GitHub Codespaces
-
-This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
-
-To get started:
-
-- Open the repo in [Codespaces](https://github.com/nf-core/tada/codespaces)
-- Tools installed
-  - nf-core
-  - Nextflow
-
-Devcontainer specs:
-
-- [DevContainer config](.devcontainer/devcontainer.json)

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,15 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/tada/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/h3abionet/TADA/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/tada/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/tada _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/h3abionet/TADA/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/ci.yml

@@ -18,8 +18,8 @@ concurrency:
 jobs:
   test:
     name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/tada') }}"
+    # Only run on push if this is the dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'h3abionet/TADA') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

README.md

@@ -1,24 +1,15 @@
-<h1>
-  <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-tada_logo_dark.png">
-    <img alt="nf-core/tada" src="docs/images/nf-core-tada_logo_light.png">
-  </picture>
-</h1>
-
 [![GitHub Actions CI Status](https://github.com/nf-core/tada/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/tada/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/tada/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/tada/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/tada/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
-[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
-[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/tada)
-
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23tada-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/tada)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+<!-- [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) -->
+<!-- [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) -->
+<!-- [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) -->
+<!-- [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -->
+<!-- [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/tada) -->
 
 ## Introduction
 
-**nf-core/tada** is a bioinformatics pipeline that ...
+**TADA** is a bioinformatics pipeline that ...
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
@@ -38,9 +29,6 @@
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
@@ -52,14 +40,14 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
+
 
 Now, you can run the pipeline using:
 
 <!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
 
 ```bash
-nextflow run nf-core/tada \
+nextflow run h3abionet/TADA \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -89,21 +77,16 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on the [Slack `#tada` channel](https://nfcore.slack.com/channels/tada) (you can join with [this invite](https://nf-co.re/join/slack)).
-
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/tada for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
-
-You can cite the `nf-core` publication as follows:
-
-> **The nf-core framework for community-curated bioinformatics pipelines.**
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+
+> The nf-core framework for community-curated bioinformatics pipelines.
 >
 > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
 >
-> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
+ 
+In addition, references of tools and data used in this pipeline are as follows:
+
+...

docs/usage.md

@@ -1,7 +1,5 @@
 # nf-core/tada: Usage
 
-## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/tada/usage](https://nf-co.re/tada/usage)
-
 > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
 
 ## Introduction
@@ -167,7 +165,7 @@ You can also supply a run name to resume a specific run: `-resume [run-name]`. U
 
 ### `-c`
 
-Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
+Specify the path to a specific config file (this is a core Nextflow command). 
 
 ## Custom configuration
 
@@ -195,8 +193,6 @@ In most cases, you will only need to create a custom config as a one-off but if
 
 See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
 
-If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
-
 ## Azure Resource Requests
 
 To be used with the `azurebatch` profile by specifying the `-profile azurebatch`.