Merge pull request #1 from phac-nml/update/code-for-clustering

Update/code for clustering

.github/CONTRIBUTING.md

@@ -1,17 +1,17 @@
-# phac-nml/iridanextexample: Contributing Guidelines
+# phac-nml/gasclustering: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving phac-nml/iridanextexample.
+Many thanks for taking an interest in improving phac-nml/gasclustering.
 
-We try to manage the required tasks for phac-nml/iridanextexample using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for phac-nml/gasclustering using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 ## Contribution workflow
 
-If you'd like to write some code for phac-nml/iridanextexample, the standard workflow is as follows:
+If you'd like to write some code for phac-nml/gasclustering, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [phac-nml/iridanextexample issues](https://github.com/phac-nml/iridanextexample/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 [phac-nml/iridanextexample repository](https://github.com/phac-nml/iridanextexample) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [phac-nml/gasclustering issues](https://github.com/phac-nml/gasclustering/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 [phac-nml/gasclustering repository](https://github.com/phac-nml/gasclustering) 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
@@ -52,11 +52,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [phac-nml/iridanextexample documentation](https://github.com/phac-nml/iridanextexample/).
+For further information/help, please consult the [phac-nml/gasclustering documentation](https://github.com/phac-nml/gasclustering/).
 
 ## Pipeline contribution conventions
 
-To make the phac-nml/iridanextexample 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 phac-nml/gasclustering 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
 
@@ -105,7 +105,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/phac-nml/iridanextexample/codespaces)
+- Open the repo in [Codespaces](https://github.com/phac-nml/gasclustering/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -44,4 +44,4 @@ 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 phac-nml/iridanextexample _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of phac-nml/gasclustering _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
 contact_links:
   - name: "GitHub"
-    url: https://github.com/phac-nml/iridanextexample
+    url: https://github.com/phac-nml/gasclustering
     about: The GitHub page for development.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the phac-nml/iridanextexample pipeline
+description: Suggest an idea for the phac-nml/gasclustering pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# phac-nml/iridanextexample pull request
+# phac-nml/gasclustering pull request
 
-Many thanks for contributing to phac-nml/iridanextexample!
+Many thanks for contributing to phac-nml/gasclustering!
 
 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/phac-nml/iridanextexample/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/phac-nml/gasclustering/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/phac-nml/iridanextexample/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/phac-nml/gasclustering/tree/main/.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

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the phac-nml repo main branch are only ok if coming from the phac-nml repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'phac-nml/iridanextexample'
+        if: github.repository == 'phac-nml/gasclustering'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/iridanextexample ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/gasclustering ]] && [[ $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 phac-nml dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/iridanextexample') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/gasclustering') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

.nf-core.yml

@@ -2,15 +2,15 @@ repository_type: pipeline
 
 lint:
   files_exist:
-    - assets/nf-core-iridanextexample_logo_light.png
-    - docs/images/nf-core-iridanextexample_logo_light.png
-    - docs/images/nf-core-iridanextexample_logo_dark.png
+    - assets/nf-core-gasclustering_logo_light.png
+    - docs/images/nf-core-gasclustering_logo_light.png
+    - docs/images/nf-core-gasclustering_logo_dark.png
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
     - lib/NfcoreTemplate.groovy
-    - lib/WorkflowIridanextexample.groovy
+    - lib/WorkflowGasclustering.groovy
   files_unchanged:
     - assets/sendmail_template.txt
     - assets/email_template.html

CHANGELOG.md

@@ -1,4 +1,4 @@
-# phac-nml/iridanextexample: Changelog
+# phac-nml/gasclustering: 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).
@@ -23,7 +23,7 @@ Allowing non-gzipped FASTQ files as input. Default branch is now main.
 
 ## 1.0.0 - 2023/11/30
 
-Initial release of phac-nml/iridanextexample, created with the [nf-core](https://nf-co.re/) template.
+Initial release of phac-nml/gasclustering, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# phac-nml/iridanextexample: Citations
+# phac-nml/gasclustering: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

README.md

@@ -25,7 +25,7 @@ Other parameters (defaults from nf-core) are defined in [nextflow_schema.json](n
 To run the pipeline, please do:
 
 ```bash
-nextflow run phac-nml/iridanextexample -profile singularity -r main -latest --input assets/samplesheet.csv --outdir results
+nextflow run phac-nml/gasclustering -profile singularity -r main -latest --input assets/samplesheet.csv --outdir results
 ```
 
 Where the `samplesheet.csv` is structured as specified in the [Input](#input) section.
@@ -90,7 +90,7 @@ There is also a pipeline execution summary output file provided (specified in th
 To run with the test profile, please do:
 
 ```bash
-nextflow run phac-nml/iridanextexample -profile docker,test -r main -latest --outdir results
+nextflow run phac-nml/gasclustering -profile docker,test -r main -latest --outdir results
 ```
 
 # Legal

assets/adaptivecard.json

@@ -17,7 +17,7 @@
                         "size": "Large",
                         "weight": "Bolder",
                         "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
-                        "text": "phac-nml/iridanextexample v${version} - ${runName}",
+                        "text": "phac-nml/gasclustering v${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="phac-nml/iridanextexample: Example IRIDA Next pipeline">
-  <title>phac-nml/iridanextexample Pipeline Report</title>
+  <meta name="description" content="phac-nml/gasclustering: Example IRIDA Next pipeline">
+  <title>phac-nml/gasclustering 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>phac-nml/iridanextexample v${version}</h1>
+<h1>phac-nml/gasclustering v${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;">phac-nml/iridanextexample execution completed unsuccessfully!</h4>
+        <h4 style="margin-top:0; color: inherit;">phac-nml/gasclustering 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;">phac-nml/iridanextexample execution co
 } else {
     out << """
     <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        phac-nml/iridanextexample execution completed successfully!
+        phac-nml/gasclustering execution completed successfully!
     </div>
     """
 }
@@ -44,8 +44,8 @@ <h3>Pipeline Configuration:</h3>
     </tbody>
 </table>
 
-<p>phac-nml/iridanextexample</p>
-<p><a href="https://github.com/phac-nml/iridanextexample">https://github.com/phac-nml/iridanextexample</a></p>
+<p>phac-nml/gasclustering</p>
+<p><a href="https://github.com/phac-nml/gasclustering">https://github.com/phac-nml/gasclustering</a></p>
 
 </div>
 

assets/email_template.txt

@@ -4,15 +4,15 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  phac-nml/iridanextexample v${version}
+  phac-nml/gasclustering v${version}
 ----------------------------------------------------
 Run Name: $runName
 
 <% if (success){
-    out << "## phac-nml/iridanextexample execution completed successfully! ##"
+    out << "## phac-nml/gasclustering execution completed successfully! ##"
 } else {
     out << """####################################################
-## phac-nml/iridanextexample execution completed unsuccessfully! ##
+## phac-nml/gasclustering execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -35,5 +35,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-phac-nml/iridanextexample
-https://github.com/phac-nml/iridanextexample
+phac-nml/gasclustering
+https://github.com/phac-nml/gasclustering

assets/methods_description_template.yml

@@ -1,11 +1,11 @@
 id: "nf-core-iridanext-methods-description"
 description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
-section_name: "phac-nml/iridanextexample Methods Description"
-section_href: "https://github.com/phac-nml/iridanextexample"
+section_name: "phac-nml/gasclustering Methods Description"
+section_href: "https://github.com/phac-nml/gasclustering"
 plot_type: "html"
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using phac-nml/iridanextexample v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using phac-nml/gasclustering v${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

@@ -1,13 +1,13 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/phac-nml/iridanextexample/releases/tag/dev" target="_blank">phac-nml/iridanextexample</a>
+  This report has been generated by the <a href="https://github.com/phac-nml/gasclustering/releases/tag/dev" target="_blank">phac-nml/gasclustering</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://github.com/phac-nml/iridanextexample/" target="_blank">documentation</a>.
+  <a href="https://github.com/phac-nml/gasclustering/" target="_blank">documentation</a>.
 report_section_order:
-  "phac-nml-iridanextexample-methods-description":
+  "phac-nml-gasclustering-methods-description":
     order: -1000
   software_versions:
     order: -1001
-  "phac-nml-iridanextexample-summary":
+  "phac-nml-gasclustering-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/phac-nml/iridanextexample/main/assets/schema_input.json",
-    "title": "phac-nml/iridanextexample pipeline - params.input schema",
+    "$id": "https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/schema_input.json",
+    "title": "phac-nml/gasclustering pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "phac-nml/iridanextexample v${version} - ${runName}",
+            "author_name": "phac-nml/gasclustering v${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 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    phac-nml/iridanextexample Nextflow base config file
+    phac-nml/gasclustering 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

conf/test.config

@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run phac-nml/iridanextexample -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run phac-nml/gasclustering -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -20,5 +20,5 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv'
+    input  = 'https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/samplesheet.csv'
 }

conf/test_full.config

@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run phac-nml/iridanextexample -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run phac-nml/gasclustering -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = 'https://raw.githubusercontent.com/phac-nml/iridanextexample/main/assets/samplesheet.csv'
+    input = 'https://raw.githubusercontent.com/phac-nml/gasclustering/main/assets/samplesheet.csv'
 }

docs/README.md

@@ -1,6 +1,6 @@
-# phac-nml/iridanextexample: Documentation
+# phac-nml/gasclustering: Documentation
 
-The phac-nml/iridanextexample documentation is split into the following pages:
+The phac-nml/gasclustering documentation is split into the following pages:
 
 - [Usage](usage.md)
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.

docs/output.md

@@ -1,4 +1,4 @@
-# phac-nml/iridanextexample: Output
+# phac-nml/gasclustering: Output
 
 ## Introduction
 

docs/run-wes-example.json

@@ -13,6 +13,6 @@
         "engine": "nextflow",
         "execute_loc": "azure"
     },
-    "workflow_url": "https://github.com/phac-nml/iridanextexample",
+    "workflow_url": "https://github.com/phac-nml/gasclustering",
     "workflow_attachment": ""
 }