h3abionet -> HPCBio

Author: cjfields

.github/CONTRIBUTING.md

@@ -13,8 +13,8 @@ Contributions to the code are even more welcome ;)
 
 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 [h3abionet/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 [h3abionet/TADA repository](https://github.com/h3abionet/TADA) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [HPCBio/TADA issues](https://github.com/HPCBio/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 [HPCBio/TADA repository](https://github.com/HPCBio/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
@@ -55,11 +55,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [TADA documentation](https://github.com/h3abionet/TADA/usage).
+For further information/help, please consult the [TADA documentation](https://github.com/HPCBio/TADA/usage).
 
 ## Pipeline contribution conventions
 
-To make the h3abionet/TADA code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the HPCBio/TADA code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [h3abionet/TADA pipeline documentation](https://github.com/h3abionet/TADA/usage)
+        - [HPCBio/TADA pipeline documentation](https://github.com/HPCBio/TADA/usage)
 
   - type: textarea
     id: description
@@ -47,4 +47,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of h3abionet/TADA _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of HPCBio/TADA _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the h3abionet/TADA pipeline
+description: Suggest an idea for the HPCBio/TADA pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# h3abionet/TADA pull request
+# HPCBio/TADA pull request
 
-Many thanks for contributing to h3abionet/TADA!
+Many thanks for contributing to HPCBio/TADA!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 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/h3abionet/TADA/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/HPCBio/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/h3abionet/TADA/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/HPCBio/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/branch.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'h3abionet/TADA'
+        if: github.repository == 'HPCBio/TADA'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == h3abionet/TADA ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == HPCBio/TADA ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'h3abionet/TADA'
+      github.repository == 'HPCBio/TADA'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/h3abionet/TADA/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/HPCBio/TADA/actions/runs/${{ github.run_id }}) for more details.

CHANGELOG.md

@@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0dev - [date]
 
-Initial release of h3abionet/TADA, created with the [nf-core](https://nf-co.re/) template.
+Initial release of HPCBio/TADA, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# h3abionet/TADA: Citations
+# HPCBio/TADA: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

README.md

@@ -1,11 +1,11 @@
-[![GitHub Actions CI Status](https://github.com/h3abionet/TADA/actions/workflows/ci.yml/badge.svg)](https://github.com/h3abionet/TADA/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/h3abionet/TADA/actions/workflows/linting.yml/badge.svg)](https://github.com/h3abionet/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)
+[![GitHub Actions CI Status](https://github.com/HPCBio/TADA/actions/workflows/ci.yml/badge.svg)](https://github.com/HPCBio/TADA/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/HPCBio/TADA/actions/workflows/linting.yml/badge.svg)](https://github.com/HPCBio/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/h3abionet/TADA) -->
+<!-- [![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/HPCBio/TADA) -->
 
 ## Introduction
 
@@ -47,7 +47,7 @@ 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 h3abionet/TADA \
+nextflow run HPCBio/TADA \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -67,7 +67,7 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-h3abionet/TADA was originally written by Chris Fields.
+HPCBio/TADA was originally written by Chris Fields.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 

assets/adaptivecard.json

@@ -17,7 +17,7 @@
                         "size": "Large",
                         "weight": "Bolder",
                         "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "h3abionet/TADA v${version} - ${runName}",
+                        "text": "HPCBio/TADA v${version} - ${runName}",
                         "wrap": true
                     },
                     {