Merge pull request #832 from nf-core/dev

Dev -> Master for v3.8 release
nf-core · May 25, 2022 · 6995330 · 6995330
2 parents e0dfce9 + 8f59050
commit 6995330
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diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/rnaseq'
         run: |
-          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnaseq ]] && [[ $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
@@ -42,4 +42,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-#
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -143,5 +143,3 @@ jobs:
       - name: Run pipeline with Salmon and various parameters
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
-
-#
diff --git a/.github/workflows/fix-linting.yml b/.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/rnaseq'
+    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
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -48,7 +48,7 @@ jobs:
           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"
@@ -78,5 +78,3 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-
-#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -26,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-#
diff --git a/.prettierignore b/.prettierignore
@@ -1,3 +1,4 @@
+email_template.html
 .nextflow*
 work/
 data/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,27 @@
 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).
 
+## [[3.8](https://github.com/nf-core/rnaseq/releases/tag/3.8)] - 2022-05-25
+
+### :warning: Major enhancements
+
+Fixed quite a well hidden bug in the UMI processing mode of the pipeline when using `--with_umi --aligner star_salmon` as reported by [Lars Roed Ingerslev](https://github.com/lars-work-sund). Paired-end BAM files were not appropriately name sorted after `umi_tools dedup` which ultimately resulted in incorrect reading and quantification with Salmon. If you have used previous versions of the pipeline to analyse paired-end UMI data it will need to be reprocessed using this version of the pipeline. See [#828](https://github.com/nf-core/rnaseq/issues/828) for more context.
+
+### Enhancements & fixes
+
+- [[#824](https://github.com/nf-core/rnaseq/issues/824)] - Add explicit docs for usage of featureCounts in the pipeline
+- [[#825](https://github.com/nf-core/rnaseq/issues/825)] - Pipeline fails due to trimming related removal of all reads from a sample
+- [[#827](https://github.com/nf-core/rnaseq/issues/827)] - Control generation of --output-stats when running umi-tools dedup
+- [[#828](https://github.com/nf-core/rnaseq/issues/828)] - Filter BAM output of UMI-tools dedup before passing to Salmon quant
+- Updated pipeline template to [nf-core/tools 2.4.1](https://github.com/nf-core/tools/releases/tag/2.4.1)
+
+### Parameters
+
+| Old parameter | New parameter            |
+| ------------- | ------------------------ |
+|               | `--min_trimmed_reads`    |
+|               | `--umitools_dedup_stats` |
+
 ## [[3.7](https://github.com/nf-core/rnaseq/releases/tag/3.7)] - 2022-05-03
 
 ### :warning: Major enhancements

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Phil Ewels, Rickard Hammarén
+Copyright (c) Harshil Patel, Phil Ewels, Rickard Hammarén
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -2,17 +2,18 @@
 
 [![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/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/rnaseq/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1400710)
-
-[![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%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)
-[![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/rnaseq/results)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1400710-1073c8)](https://doi.org/10.5281/zenodo.1400710)
+
+[![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/rnaseq)
+
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?logo=slack)](https://nfcore.slack.com/channels/rnaseq)
+[![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)
 
 ## Introduction
 

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -1,33 +1,24 @@
 <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/rnaseq: Nextflow RNA-Seq analysis pipeline, part of the nf-core community." />
-    <title>nf-core/rnaseq 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/rnaseq: Nextflow RNA-Seq analysis pipeline, part of the nf-core community.">
+  <title>nf-core/rnaseq Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-      <h1>nf-core/rnaseq 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/rnaseq execution completed unsuccessfully!</h4>
+<h1>nf-core/rnaseq v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/rnaseq execution completed unsuccessfully!</h4>
         <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
         <p>The full error message was:</p>
         <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
@@ -69,67 +60,26 @@ <h4 style="margin-top: 0; color: inherit">nf-core/rnaseq execution completed wit
         "
       >
         nf-core/rnaseq 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/rnaseq</p>
-      <p><a href="https://github.com/nf-core/rnaseq">https://github.com/nf-core/rnaseq</a></p>
-    </div>
-  </body>
+<p>nf-core/rnaseq</p>
+<p><a href="https://github.com/nf-core/rnaseq">https://github.com/nf-core/rnaseq</a></p>
+
+</div>
+
+</body>
 </html>
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -28,6 +28,7 @@ run_modules:
 
 # Order of modules
 top_modules:
+  - "fail_trimmed_samples"
   - "fail_mapped_samples"
   - "fail_strand_check"
   - "star_rsem_deseq2_pca"
@@ -140,6 +141,15 @@ sp:
 
 # See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
 custom_data:
+  fail_trimmed_samples:
+    section_name: "WARNING: Fail Trimming Check"
+    description: "List of samples that failed the minimum trimmed reads threshold specified via the '--min_trimmed_reads' parameter, and hence were ignored for the downstream processing steps."
+    plot_type: "table"
+    pconfig:
+      id: "fail_trimmed_samples_table"
+      table_title: "Samples failed trimming threshold"
+      namespace: "Samples failed trimming threshold"
+      format: "{:.0f}"
   fail_mapped_samples:
     section_name: "WARNING: Fail Alignment Check"
     description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."