Rename to nf-cmgg/smallvariants

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# nf-cmgg/germline: Contributing Guidelines
+# nf-cmgg/smallvariants: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-cmgg/germline.
+Many thanks for taking an interest in improving nf-cmgg/smallvariants.
 
-We try to manage the required tasks for nf-cmgg/germline using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-cmgg/smallvariants 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 nf-cmgg/germline, the standard workflow is as follows:
+If you'd like to write some code for nf-cmgg/smallvariants, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-cmgg/germline issues](https://github.com/nf-cmgg/germline/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-cmgg/germline repository](https://github.com/nf-cmgg/germline) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-cmgg/smallvariants issues](https://github.com/nf-cmgg/smallvariants/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-cmgg/smallvariants repository](https://github.com/nf-cmgg/smallvariants) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines 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
@@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the nf-cmgg/germline 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 nf-cmgg/smallvariants 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
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-cmgg/germline/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-cmgg/smallvariants/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -39,4 +39,4 @@ 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 nf-cmgg/germline _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-cmgg/smallvariants _(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 nf-cmgg/germline pipeline
+description: Suggest an idea for the nf-cmgg/smallvariants pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# nf-cmgg/germline pull request
+# nf-cmgg/smallvariants pull request
 
-Many thanks for contributing to nf-cmgg/germline!
+Many thanks for contributing to nf-cmgg/smallvariants!
 
 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/nf-cmgg/germline/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/smallvariants/tree/main/.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-cmgg/germline/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/smallvariants/tree/main/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core pipelines 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

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-cmgg/germline'
+        if: github.repository == 'nf-cmgg/smallvariants'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/germline ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-cmgg/smallvariants ]] && [[ $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/build-docs.yml

@@ -57,7 +57,6 @@ jobs:
         if: ${{ github.head_ref || github.ref_name }} == 'main'
         run: |
           mike deploy --push --update-aliases ${{ steps.version.outputs.version }} latest
-
 
       - name: Set default docs
         run: mike set-default --push latest

.github/workflows/ci.yml

@@ -19,7 +19,7 @@ jobs:
   test_all:
     name: Run ${{ matrix.filter }} tests | shard ${{ matrix.shard }} (${{ matrix.NXF_VER }})
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/germline') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/smallvariants') }}"
     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 == 'nf-cmgg/germline'
+      github.repository == 'nf-cmgg/smallvariants'
     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/nf-cmgg/germline/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/nf-cmgg/smallvariants/actions/runs/${{ github.run_id }}) for more details.

.nf-core.yml

@@ -3,9 +3,9 @@ lint:
   actions_ci: false
   files_exist:
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_light.png
-    - docs/images/nf-core-germline_logo_dark.png
+    - assets/nf-core-smallvariants_logo_light.png
+    - docs/images/nf-core-smallvariants_logo_light.png
+    - docs/images/nf-core-smallvariants_logo_dark.png
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
@@ -33,14 +33,14 @@ nf_core_version: 3.0.2
 repository_type: pipeline
 template:
   author: nvnieuwk
-  description: A nextflow pipeline for calling and annotating small germline variants
-    from short DNA reads for WES and WGS data
+  description: A nextflow pipeline for calling and annotating small smallvariants
+    variants from short DNA reads for WES and WGS data
   force: false
   is_nfcore: false
-  name: germline
+  name: smallvariants
   org: nf-cmgg
   outdir: .
   skip_features:
     - fastqc
     - is_nfcore
-  version: 1.10.0dev
+  version: 2.0.0dev

CHANGELOG.md

@@ -1,4 +1,4 @@
-# nf-cmgg/germline: Changelog
+# nf-cmgg/smallvariants: 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).
@@ -41,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 1. Added the `--squash-ploidy` argument to the RTG vcfeval process.
 2. Update to nf-core v3.0.1
-3. Completely reworked the output directory structure to a more sensible structure. The pipeline can now be run on the same output directory every time and will incrementally add files to the correct family folder. See the [output documentation](https://nf-cmgg.github.io/germline/latest/output/) for more info.
+3. Completely reworked the output directory structure to a more sensible structure. The pipeline can now be run on the same output directory every time and will incrementally add files to the correct family folder. See the [output documentation](https://nf-cmgg.github.io/smallvariants/latest/output/) for more info.
 4. Migrated to the new workflow output definitions.
 5. Bumped the minimal Nextflow version to 24.10.0.
 6. Added the somalier reports to the multiQC report.
@@ -105,8 +105,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### New features
 
 1. Added UPDio for Uniparental Disomy detection in family samples. This introduces the `--updio` parameter to turn on this detection and `--updio_common_cnvs` to supply a common CNVs file to UPDio. The family needs to contain at least one child with its mother and father.
-2. Added docs built with MkDocs. See the documentation [site](https://nf-cmgg.github.io/germline/latest) here.
-3. Added AutoMap to find regions of homozygosity from human samples. This introduces the `--automap` parameter to turn on this feature and the `--automap_repeats`, `--automap_panel` and `--automap_panel_name` parameters to configure AutoMap (see the [parameters](https://nf-cmgg.github.io/germline/latest/parameters) docs for more information)
+2. Added docs built with MkDocs. See the documentation [site](https://nf-cmgg.github.io/smallvariants/latest) here.
+3. Added AutoMap to find regions of homozygosity from human samples. This introduces the `--automap` parameter to turn on this feature and the `--automap_repeats`, `--automap_panel` and `--automap_panel_name` parameters to configure AutoMap (see the [parameters](https://nf-cmgg.github.io/smallvariants/latest/parameters) docs for more information)
 
 ### Changes
 

README.md

@@ -1,19 +1,19 @@
-# nf-cmgg/germline
+# nf-cmgg/smallvariants
 
-[![GitHub Actions CI Status](https://github.com/nf-cmgg/germline/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-cmgg/germline/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml)
+[![GitHub Actions CI Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/smallvariants/actions/workflows/linting.yml)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.0-23aa62.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 Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/germline)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-cmgg/smallvariants)
 
 ## Introduction
 
-**nf-cmgg/germline** is a nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data.
+**nf-cmgg/smallvariants** is a nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
-Please have a look at the [documentation](https://nf-cmgg.github.io/germline/latest/) on how to run the pipeline.
+Please have a look at the [documentation](https://nf-cmgg.github.io/smallvariants/latest/) on how to run the pipeline.

assets/adaptivecard.json

@@ -17,7 +17,7 @@
                         "size": "Large",
                         "weight": "Bolder",
                         "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "nf-cmgg/germline v${version} - ${runName}",
+                        "text": "nf-cmgg/smallvariants v${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="nf-cmgg/germline: A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data">
-  <title>nf-cmgg/germline Pipeline Report</title>
+  <meta name="description" content="nf-cmgg/smallvariants: A nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data">
+  <title>nf-cmgg/smallvariants 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>nf-cmgg/germline ${version}</h1>
+<h1>nf-cmgg/smallvariants ${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;">nf-cmgg/germline execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">nf-cmgg/smallvariants 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;">nf-cmgg/germline execution completed u
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-cmgg/germline execution completed successfully!
+        nf-cmgg/smallvariants execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>nf-cmgg/germline</p>
-<p><a href="https://github.com/nf-cmgg/germline">https://github.com/nf-cmgg/germline</a></p>
+<p>nf-cmgg/smallvariants</p>
+<p><a href="https://github.com/nf-cmgg/smallvariants">https://github.com/nf-cmgg/smallvariants</a></p>
 
 </div>
 

assets/email_template.txt

@@ -1,10 +1,10 @@
 Run Name: $runName
 
 <% if (success){
-    out << "## nf-cmgg/germline execution completed successfully! ##"
+    out << "## nf-cmgg/smallvariants execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf-cmgg/germline execution completed unsuccessfully! ##
+## nf-cmgg/smallvariants 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") %>
 
 --
-nf-cmgg/germline
-https://github.com/nf-cmgg/germline
+nf-cmgg/smallvariants
+https://github.com/nf-cmgg/smallvariants

assets/methods_description_template.yml

@@ -1,11 +1,11 @@
-id: "nf-cmgg-germline-methods-description"
+id: "nf-cmgg-smallvariants-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "nf-cmgg/germline Methods Description"
-section_href: "https://github.com/nf-cmgg/germline"
+section_name: "nf-cmgg/smallvariants Methods Description"
+section_href: "https://github.com/nf-cmgg/smallvariants"
 plot_type: "html"
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-cmgg/germline v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using nf-cmgg/smallvariants v${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/nf-cmgg/germline" target="_blank">nf-cmgg/germline</a>
+  This report has been generated by the <a href="https://github.com/nf-cmgg/smallvariants" target="_blank">nf-cmgg/smallvariants</a>
   analysis pipeline.
 report_section_order:
-  "nf-cmgg-germline-methods-description":
+  "nf-cmgg-smallvariants-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "nf-cmgg-germline-summary":
+  "nf-cmgg-smallvariants-summary":
     order: -1002
 
 export_plots: true