Merging template 2.4.0

.github/workflows/awsfulltest.yml

@@ -25,6 +25,3 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -23,6 +23,3 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/smrnaseq'
         run: |
-          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/smrnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/smrnaseq ]] && [[ $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

@@ -0,0 +1,55 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  deploy:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/smrnaseq'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix linting with Prettier"
+          git push

.github/workflows/linting.yml

@@ -47,7 +47,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - uses: actions/setup-python@v1
+
+      - uses: actions/setup-python@v3
         with:
           python-version: "3.6"
           architecture: "x64"

.prettierignore

@@ -0,0 +1,9 @@
+email_template.html
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc

README.md

@@ -1,18 +1,19 @@
-# ![nf-core/smrnaseq](docs/images/nf-core/smrnaseq_logo_light.png#gh-light-mode-only) ![nf-core/smrnaseq](docs/images/nf-core/smrnaseq_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/smrnaseq](docs/images/nf-core-smrnaseq_logo_light.png#gh-light-mode-only) ![nf-core/smrnaseq](docs/images/nf-core-smrnaseq_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/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%A521.10.3-23aa62.svg?labelColor=000000)](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/)
-
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23smrnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/smrnaseq)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/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)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX)
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](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/nf-core/smrnaseq)
+
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23smrnaseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/smrnaseq)
+[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core)
+[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core)
 
 [![DOI](https://zenodo.org/badge/140590861.svg)](https://zenodo.org/badge/latestdoi/140590861)
 

assets/email_template.html

@@ -1,111 +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">
 
-    <!-- prettier-ignore -->
-    <meta name="description" content="nf-core/smrnaseq: Small RNA-Seq Best Practice Analysis Pipeline." />
-    <title>nf-core/smrnaseq 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/smrnaseq: Small RNA-Seq Best Practice Analysis Pipeline.">
+  <title>nf-core/smrnaseq Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-      <h1>nf-core/smrnaseq v${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/smrnaseq execution completed unsuccessfully!</h4>
+<h1>nf-core/smrnaseq v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/smrnaseq execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$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/smrnaseq 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/smrnaseq</p>
-      <p><a href="https://github.com/nf-core/smrnaseq">https://github.com/nf-core/smrnaseq</a></p>
-    </div>
-  </body>
+<p>nf-core/smrnaseq</p>
+<p><a href="https://github.com/nf-core/smrnaseq">https://github.com/nf-core/smrnaseq</a></p>
+
+</div>
+
+</body>
 </html>

bin/check_samplesheet.py

@@ -40,12 +40,10 @@ def print_error(error, context="Line", context_str=""):
 def check_samplesheet(file_in, file_out):
     """
     This function checks that the samplesheet follows the following structure:
-
     sample,fastq_1
     SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz
     SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz
     SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz
-
     For an example see:
     https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
     """

nextflow.config

@@ -183,7 +183,7 @@ trace {
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {