nf-core · nf-core-bot · Apr 30, 2025
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -4,44 +4,23 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/bactmap' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/bactmap' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
@@ -52,12 +31,12 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bactmap/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bactmap/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bactmap/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bactmap/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -83,5 +83,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,16 +1,13 @@
-repository_type: pipeline
-
-nf_core_version: 3.2.0
-
 lint: {}
-
+nf_core_version: 3.2.1
+repository_type: pipeline
 template:
-  org: nf-core
-  name: bactmap
-  description: A mapping-based pipeline for bacterial whole genome sequences
   author: Andries J. van Tonder
-  version: 2.0.0dev
-  force: true
+  description: A mapping-based pipeline for bacterial whole genome sequences
+  force: false
+  is_nfcore: true
+  name: bactmap
+  org: nf-core
   outdir: .
   skip_features: []
-  is_nfcore: true
+  version: 2.0.0dev
diff --git a/assets/email_template.html b/assets/email_template.html
@@ -1,110 +1,53 @@
 <html>
-  <head>
-    <meta charset="utf-8" />
-    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
-    <meta name="viewport" content="width=device-width, initial-scale=1" />
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
 
-    <meta name="description" content="nf-core/bactmap: A mapping-based pipeline for bacterial whole genome sequences" />
-    <title>nf-core/bactmap 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" />
+  <meta name="description" content="nf-core/bactmap: A mapping-based pipeline for bacterial whole genome sequences">
+  <title>nf-core/bactmap Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-      <h1>nf-core/bactmap ${version}</h1>
-      <h2>Run Name: $runName</h2>
+<img src="cid:nfcorepipelinelogo">
 
-      <% 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-core/bactmap execution completed unsuccessfully!</h4>
+<h1>nf-core/bactmap ${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/bactmap execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
-        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
-      </div>
-      """ } else { out << """
-      <div
-        style="
-          color: #3c763d;
-          background-color: #dff0d8;
-          border-color: #d6e9c6;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+    </div>
+    """
+} 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-core/bactmap execution completed successfully!
-      </div>
-      """ } %>
+    </div>
+    """
+}
+%>
 
-      <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-      <p>The command used to launch the workflow was as follows:</p>
-      <pre
-        style="
-          white-space: pre-wrap;
-          overflow: visible;
-          background-color: #ededed;
-          padding: 15px;
-          border-radius: 4px;
-          margin-bottom: 30px;
-        "
-      >
-$commandLine</pre
-      >
+<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+<p>The command used to launch the workflow was as follows:</p>
+<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
 
-      <h3>Pipeline Configuration:</h3>
-      <table
-        style="
-          width: 100%;
-          max-width: 100%;
-          border-spacing: 0;
-          border-collapse: collapse;
-          border: 0;
-          margin-bottom: 30px;
-        "
-      >
-        <tbody style="border-bottom: 1px solid #ddd">
-          <% out << summary.collect{ k,v -> "
-          <tr>
-            <th
-              style="
-                text-align: left;
-                padding: 8px 0;
-                line-height: 1.42857143;
-                vertical-align: top;
-                border-top: 1px solid #ddd;
-              "
-            >
-              $k
-            </th>
-            <td
-              style="
-                text-align: left;
-                padding: 8px;
-                line-height: 1.42857143;
-                vertical-align: top;
-                border-top: 1px solid #ddd;
-              "
-            >
-              <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
-            </td>
-          </tr>
-          " }.join("\n") %>
-        </tbody>
-      </table>
+<h3>Pipeline Configuration:</h3>
+<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
+    <tbody style="border-bottom: 1px solid #ddd;">
+        <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
+    </tbody>
+</table>
 
-      <p>nf-core/bactmap</p>
-      <p><a href="https://github.com/nf-core/bactmap">https://github.com/nf-core/bactmap</a></p>
-    </div>
-  </body>
+<p>nf-core/bactmap</p>
+<p><a href="https://github.com/nf-core/bactmap">https://github.com/nf-core/bactmap</a></p>
+
+</div>
+
+</body>
 </html>
diff --git a/assets/nf-core-bactmap_logo_light.png b/assets/nf-core-bactmap_logo_light.png
diff --git a/docs/images/nf-core-bactmap_logo_dark.png b/docs/images/nf-core-bactmap_logo_dark.png
diff --git a/docs/images/nf-core-bactmap_logo_light.png b/docs/images/nf-core-bactmap_logo_light.png
diff --git a/nextflow.config b/nextflow.config
@@ -249,7 +249,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-03-13T14:15:46+00:00",
+            "datePublished": "2025-04-30T12:25:50+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-bactmap_logo_dark.png\">\n    <img alt=\"nf-core/bactmap\" src=\"docs/images/nf-core-bactmap_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/bactmap/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/bactmap/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/bactmap/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/bactmap/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/bactmap/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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-core/bactmap)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bactmap-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/bactmap)[![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)\n\n## Introduction\n\n**nf-core/bactmap** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/bactmap \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/bactmap/usage) and the [parameter documentation](https://nf-co.re/bactmap/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/bactmap/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/bactmap/output).\n\n## Credits\n\nnf-core/bactmap was originally written by Andries J. van Tonder.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#bactmap` channel](https://nfcore.slack.com/channels/bactmap) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- 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. -->\n<!-- If you use nf-core/bactmap for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#2ba10903-33af-4faa-9ee1-d7e45a8f2fc1"
+                    "@id": "#a5c89635-4eb5-448f-8d64-97e8af04e96f"
                 }
             ],
             "name": "nf-core/bactmap"
@@ -122,8 +122,13 @@
         {
             "@id": "main.nf",
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
+            "creator": [
+                {
+                    "@id": "#ajv37@shgb2monitor.vet.private.cam.ac.uk"
+                }
+            ],
             "dateCreated": "",
-            "dateModified": "2025-03-13T14:15:46Z",
+            "dateModified": "2025-04-30T12:25:50Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -160,11 +165,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#2ba10903-33af-4faa-9ee1-d7e45a8f2fc1",
+            "@id": "#a5c89635-4eb5-448f-8d64-97e8af04e96f",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#3f5008e2-1065-44ff-89de-ac416b610232"
+                    "@id": "#59ab53b9-7a7b-4769-8ff5-e7eb2f15d71b"
                 }
             ],
             "mainEntity": {
@@ -173,7 +178,7 @@
             "name": "Test suite for nf-core/bactmap"
         },
         {
-            "@id": "#3f5008e2-1065-44ff-89de-ac416b610232",
+            "@id": "#59ab53b9-7a7b-4769-8ff5-e7eb2f15d71b",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/bactmap",
             "resource": "repos/nf-core/bactmap/actions/workflows/ci.yml",
@@ -300,6 +305,12 @@
             "@type": "Organization",
             "name": "nf-core",
             "url": "https://nf-co.re/"
+        },
+        {
+            "@id": "#ajv37@shgb2monitor.vet.private.cam.ac.uk",
+            "@type": "Person",
+            "email": "ajv37@shgb2monitor.vet.private.cam.ac.uk",
+            "name": "Andries Van Tonder"
         }
     ]
 }