Update with new template using correct names

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# dx/rna: Contributing Guidelines
+# UMCUGenetics/dxnextflowrna: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving dx/rna.
+Many thanks for taking an interest in improving UMCUGenetics/dxnextflowrna.
 
-We try to manage the required tasks for dx/rna using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for UMCUGenetics/dxnextflowrna using GitHub issues, you probably came to this page when creating one.
 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 ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for dx/rna, the standard workflow is as follows:
+If you'd like to write some code for UMCUGenetics/dxnextflowrna, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [dx/rna issues](https://github.com/UMCUGenetics/DxNextflowRNA/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 [dx/rna repository](https://github.com/dx/rna) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [UMCUGenetics/dxnextflowrna issues](https://github.com/UMCUGenetics/dxnextflowrna/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 [UMCUGenetics/dxnextflowrna repository](https://github.com/UMCUGenetics/dxnextflowrna) 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
@@ -52,7 +52,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the dx/rna 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 UMCUGenetics/dxnextflowrna 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
 
@@ -102,7 +102,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/UMCUGenetics/DxNextflowRNA/codespaces)
+- Open the repo in [Codespaces](https://github.com/UMCUGenetics/dxnextflowrna/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -49,6 +49,6 @@ body:
 
       * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-      * Version of dx/rna _(eg. 1.1, 1.5, 1.8.2)_
+      * Version of UMCUGenetics/dxnextflowrna _(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 dx/rna pipeline
+description: Suggest an idea for the UMCUGenetics/dxnextflowrna pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# dx/rna pull request
+# UMCUGenetics/dxnextflowrna pull request
 
-Many thanks for contributing to dx/rna!
+Many thanks for contributing to UMCUGenetics/dxnextflowrna!
 
 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/UMCUGenetics/DxNextflowRNA/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/UMCUGenetics/dxnextflowrna/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/UMCUGenetics/DxNextflowRNA/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/UMCUGenetics/dxnextflowrna/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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ 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 == 'dx/rna'
+        if: github.repository == 'UMCUGenetics/dxnextflowrna'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == dx/rna ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == UMCUGenetics/dxnextflowrna ]] && [[ $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/ci.yml

@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'dx/rna') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'UMCUGenetics/dxnextflowrna') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

.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 == 'dx/rna'
+      github.repository == 'UMCUGenetics/dxnextflowrna'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later

.nf-core.yml

@@ -1,19 +1,19 @@
 lint:
   files_exist:
   - CODE_OF_CONDUCT.md
-  - assets/nf-core-rna_logo_light.png
-  - docs/images/nf-core-rna_logo_light.png
-  - docs/images/nf-core-rna_logo_dark.png
+  - assets/nf-core-dxnextflowrna_logo_light.png
+  - docs/images/nf-core-dxnextflowrna_logo_light.png
+  - docs/images/nf-core-dxnextflowrna_logo_dark.png
   - .github/ISSUE_TEMPLATE/config.yml
   - .github/workflows/awstest.yml
   - .github/workflows/awsfulltest.yml
   - conf/igenomes.config
   - conf/igenomes.config
   files_unchanged:
   - CODE_OF_CONDUCT.md
-  - assets/nf-core-rna_logo_light.png
-  - docs/images/nf-core-rna_logo_light.png
-  - docs/images/nf-core-rna_logo_dark.png
+  - assets/nf-core-dxnextflowrna_logo_light.png
+  - docs/images/nf-core-dxnextflowrna_logo_light.png
+  - docs/images/nf-core-dxnextflowrna_logo_dark.png
   - .github/ISSUE_TEMPLATE/bug_report.yml
   multiqc_config:
   - report_comment
@@ -26,7 +26,7 @@ lint:
   - custom_config
 repository_type: pipeline
 template:
-  prefix: dx
+  prefix: UMCUGenetics
   skip:
   - igenomes
   - nf_core_configs

CHANGELOG.md

@@ -1,11 +1,11 @@
-# dx/rna: Changelog
+# UMCUGenetics/dxnextflowrna: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## v1.0dev - [date]
 
-Initial release of dx/rna, created with the [nf-core](https://nf-co.re/) template.
+Initial release of UMCUGenetics/dxnextflowrna, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# dx/rna: Citations
+# UMCUGenetics/dxnextflowrna: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

README.md

@@ -1,15 +1,15 @@
-[![GitHub Actions CI Status](https://github.com/UMCUGenetics/DxNextflowRNA/workflows/nf-core%20CI/badge.svg)](https://github.com/UMCUGenetics/DxNextflowRNA/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/UMCUGenetics/DxNextflowRNA/workflows/nf-core%20linting/badge.svg)](https://github.com/UMCUGenetics/DxNextflowRNA/actions?query=workflow%3A%22nf-core+linting%22)[![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/UMCUGenetics/dxnextflowrna/workflows/nf-core%20CI/badge.svg)](https://github.com/UMCUGenetics/dxnextflowrna/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/UMCUGenetics/dxnextflowrna/workflows/nf-core%20linting/badge.svg)](https://github.com/UMCUGenetics/dxnextflowrna/actions?query=workflow%3A%22nf-core+linting%22)[![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/dx/rna)
+[![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/UMCUGenetics/dxnextflowrna)
 
 ## Introduction
 
-**dx/rna** is a bioinformatics pipeline that ...
+**UMCUGenetics/dxnextflowrna** 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
@@ -53,7 +53,7 @@ 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 dx/rna \
+nextflow run UMCUGenetics/dxnextflowrna \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
@@ -67,7 +67,7 @@ see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 ## Credits
 
-dx/rna was originally written by bioinformatica.
+UMCUGenetics/dxnextflowrna was originally written by UMCU Genetics.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -80,7 +80,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 ## 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  dx/rna for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use  UMCUGenetics/dxnextflowrna 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 -->
 

assets/adaptivecard.json

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

assets/email_template.html

@@ -4,21 +4,21 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="dx/rna: RNA workflow">
-  <title>dx/rna Pipeline Report</title>
+  <meta name="description" content="UMCUGenetics/dxnextflowrna: RNA Workflow">
+  <title>UMCUGenetics/dxnextflowrna Pipeline Report</title>
 </head>
 <body>
 <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
 <img src="cid:nfcorepipelinelogo">
 
-<h1>dx/rna v${version}</h1>
+<h1>UMCUGenetics/dxnextflowrna v${version}</h1>
 <h2>Run Name: $runName</h2>
 
 <% if (!success){
     out << """
     <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">dx/rna execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">UMCUGenetics/dxnextflowrna execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
@@ -27,7 +27,7 @@ <h4 style="margin-top:0; color: inherit;">dx/rna execution completed unsuccessfu
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        dx/rna execution completed successfully!
+        UMCUGenetics/dxnextflowrna execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>dx/rna</p>
-<p><a href="https://github.com/dx/rna">https://github.com/dx/rna</a></p>
+<p>UMCUGenetics/dxnextflowrna</p>
+<p><a href="https://github.com/UMCUGenetics/dxnextflowrna">https://github.com/UMCUGenetics/dxnextflowrna</a></p>
 
 </div>
 

assets/email_template.txt

@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## dx/rna execution completed successfully! ##"
+    out << "## UMCUGenetics/dxnextflowrna execution completed successfully! ##"
 } else {
     out << """####################################################
-## dx/rna execution completed unsuccessfully! ##
+## UMCUGenetics/dxnextflowrna execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -27,5 +27,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-dx/rna
-https://github.com/dx/rna
+UMCUGenetics/dxnextflowrna
+https://github.com/UMCUGenetics/dxnextflowrna

assets/methods_description_template.yml

@@ -1,13 +1,13 @@
-id: "dx-rna-methods-description"
+id: "UMCUGenetics-dxnextflowrna-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "dx/rna Methods Description"
-section_href: "https://github.com/dx/rna"
+section_name: "UMCUGenetics/dxnextflowrna Methods Description"
+section_href: "https://github.com/UMCUGenetics/dxnextflowrna"
 plot_type: "html"
 ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using dx/rna v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using UMCUGenetics/dxnextflowrna v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>

assets/multiqc_config.yml

@@ -1,12 +1,12 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/UMCUGenetics/DxNextflowRNA/releases/tag/dev" target="_blank">dx/rna</a>
+  This report has been generated by the <a href="https://github.com/UMCUGenetics/dxnextflowrna/releases/tag/dev" target="_blank">UMCUGenetics/dxnextflowrna</a>
   analysis pipeline.
 report_section_order:
-  "dx-rna-methods-description":
+  "UMCUGenetics-dxnextflowrna-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "dx-rna-summary":
+  "UMCUGenetics-dxnextflowrna-summary":
     order: -1002
 
 export_plots: true

assets/schema_input.json

@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/dx/rna/master/assets/schema_input.json",
-    "title": "dx/rna pipeline - params.input schema",
+    "$id": "https://raw.githubusercontent.com/UMCUGenetics/dxnextflowrna/master/assets/schema_input.json",
+    "title": "UMCUGenetics/dxnextflowrna pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {

assets/sendmail_template.txt

@@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="dx-rna_logo.png"
+Content-Type: image/png;name="UMCUGenetics-dxnextflowrna_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="dx-rna_logo_light.png"
+Content-Disposition: inline; filename="UMCUGenetics-dxnextflowrna_logo_light.png"
 
-<% out << new File("$projectDir/assets/dx-rna_logo_light.png").
+<% out << new File("$projectDir/assets/UMCUGenetics-dxnextflowrna_logo_light.png").
     bytes.
     encodeBase64().
     toString().

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "dx/rna v${version} - ${runName}",
+            "author_name": "UMCUGenetics/dxnextflowrna v${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

conf/base.config

@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    dx/rna Nextflow base config file
+    UMCUGenetics/dxnextflowrna Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on