Merge branch 'dev' into support-aligned-reads

2024-11-13 07:03:10 +00:00 · 2022-06-02 12:45:29 +02:00 · 2022-06-02 12:45:29 +02:00 · c9581b1796
commit c9581b1796
parent 87a1d80519 dfcaaae1fb
27 changed files with 8525 additions and 142 deletions
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@ -28,6 +28,3 @@ jobs:
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-${{ github.sha }}"
            }
          profiles: test_full,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@ -23,6 +23,3 @@ jobs:
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/taxprofiler/results-test-${{ github.sha }}"
            }
          profiles: test,aws_tower
-          nextflow_config: |
-            process.errorStrategy = 'retry'
-            process.maxRetries = 3
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@ -13,7 +13,7 @@ jobs:
      - name: Check PRs
        if: github.repository == 'nf-core/taxprofiler'
        run: |
-          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/taxprofiler ]] && [[ $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
-#
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@ -38,7 +38,7 @@ jobs:
          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
          - "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
          - "--shortread_complexityfilter_tool bbduk"
-          - "--shortread_complexityfilter_tool prinseq"
+          - "--shortread_complexityfilter_tool prinseqplusplus"
          - "--perform_runmerging"
          - "--perform_runmerging --shortread_clipmerge_mergepairs"
          - "--shortread_complexityfilter false --perform_shortread_hostremoval"
@ -71,5 +71,3 @@ jobs:
        # Remember that you can parallelise this by using strategy.matrix
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
-
-#
--- 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/taxprofiler'
+    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
--- 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
-
-#
--- 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
-#
--- a/.prettierignore
+++ b/.prettierignore
@ -1,2 +1,10 @@
+email_template.html
+.nextflow*
+work/
+data/
+results/
+.DS_Store
 testing/
+testing*
 tests/
+*.pyc
--- a/README.md
+++ b/README.md
@ -1,18 +1,19 @@
-# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_light.png#gh-light-mode-only) ![nf-core/taxprofiler](docs/images/nf-core-taxprofiler_logo_custom_dark.png#gh-dark-mode-only)

 [![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/taxprofiler/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/taxprofiler/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?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/)
+[![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/taxprofiler)

-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
-[![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)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?logo=slack)](https://nfcore.slack.com/channels/taxprofiler)
+[![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

--- a/assets/email_template.html
+++ b/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/taxprofiler: Taxonomic profiling of shotgun metagenomic data" />
-    <title>nf-core/taxprofiler 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/taxprofiler: Taxonomic profiling of shotgun metagenomic data">
+  <title>nf-core/taxprofiler Pipeline Report</title>
+</head>
+<body>
+<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">

-      <h1>nf-core/taxprofiler 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/taxprofiler execution completed unsuccessfully!</h4>
+<h1>nf-core/taxprofiler v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
        <p>The full error message was:</p>
-        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
-      </div>
-      """ } else { out << """
-      <div
-        style="
-          color: #3c763d;
-          background-color: #dff0d8;
-          border-color: #d6e9c6;
-          padding: 15px;
-          margin-bottom: 20px;
-          border: 1px solid transparent;
-          border-radius: 4px;
-        "
-      >
-        nf-core/taxprofiler execution completed successfully!
-      </div>
-      """ } %>
-
-      <p>The workflow was completed at <strong>$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
-      >
-
-      <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/taxprofiler</p>
-      <p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
    </div>
-  </body>
+    """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        nf-core/taxprofiler execution completed successfully!
+    </div>
+    """
+}
+%>
+
+<p>The workflow was completed at <strong>$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>
+
+<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/taxprofiler</p>
+<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
+
+</div>
+
+</body>
 </html>
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@ -9,3 +9,7 @@ report_section_order:
    order: -1001

 export_plots: true
+
+custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
+custom_logo_url: https://nf-co.re/taxprofiler
+custom_logo_title: "nf-core/taxprofiler"
--- a/conf/modules.config
+++ b/conf/modules.config
@ -54,7 +54,8 @@ process {
            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
            // filtering options
-            "--length_required ${params.shortread_clipmerge_minlength}"
+            "--length_required ${params.shortread_clipmerge_minlength}",
+            (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
@ -74,7 +75,8 @@ process {
            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
            params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
            // filtering options
-            "--length_required ${params.shortread_clipmerge_minlength}"
+            "--length_required ${params.shortread_clipmerge_minlength}",
+            params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
        ].join(' ').trim()
        ext.prefix = { "${meta.id}_${meta.run_accession}" }
        publishDir = [
--- a/conf/test.config
+++ b/conf/test.config
@ -29,6 +29,7 @@ params {
    perform_shortread_complexityfilter    = true
    perform_shortread_hostremoval         = true
    perform_longread_hostremoval          = true
+    perform_runmerging                    = true
    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
    run_kaiju                             = true
    run_kraken2                           = true
--- a/conf/test_nopreprocessing.config
+++ b/conf/test_nopreprocessing.config
@ -0,0 +1,46 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset skipping all preprocessing to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    perform_shortread_clipmerge           = false
+    perform_longread_clip                 = false
+    perform_shortread_complexityfilter    = false
+    perform_shortread_hostremoval         = false
+    perform_longread_hostremoval          = false
+    perform_runmerging                    = false
+    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                             = true
+    run_kraken2                           = true
+    run_malt                              = true
+    run_metaphlan3                        = true
+    run_centrifuge                        = true
+    run_diamond                           = true
+}
+
+process {
+    withName: MALT_RUN {
+        maxForks = 1
+    }
+}
--- a/conf/test_noprofiling.config
+++ b/conf/test_noprofiling.config
@ -0,0 +1,46 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset without performing any profiling to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+    // TODO nf-core: Give any required params for the test so that command line flags are not needed
+    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
+    databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
+    perform_shortread_clipmerge           = true
+    perform_longread_clip                 = true
+    perform_shortread_complexityfilter    = true
+    perform_shortread_hostremoval         = true
+    perform_longread_hostremoval          = true
+    perform_runmerging                    = true
+    hostremoval_reference                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    run_kaiju                             = false
+    run_kraken2                           = false
+    run_malt                              = false
+    run_metaphlan3                        = false
+    run_centrifuge                        = false
+    run_diamond                           = false
+}
+
+process {
+    withName: MALT_RUN {
+        maxForks = 1
+    }
+}
--- a/docs/images/nf-core-taxprofiler_icon.png
+++ b/docs/images/nf-core-taxprofiler_icon.png
--- a/docs/images/nf-core-taxprofiler_icon.svg
+++ b/docs/images/nf-core-taxprofiler_icon.svg
@ -0,0 +1,444 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="160mm"
+   height="120mm"
+   viewBox="0 0 160 120"
+   version="1.1"
+   id="svg5581"
+   inkscape:version="1.2 (1:1.2+202205241504+da316b6974)"
+   sodipodi:docname="nf-core-taxprofiler_icon.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
+     id="namedview5583"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
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--- a/docs/images/nf-core-taxprofiler_logo_custom_dark.png
+++ b/docs/images/nf-core-taxprofiler_logo_custom_dark.png
--- a/docs/images/nf-core-taxprofiler_logo_custom_dark.svg
+++ b/docs/images/nf-core-taxprofiler_logo_custom_dark.svg
--- a/docs/images/nf-core-taxprofiler_logo_custom_light.png
+++ b/docs/images/nf-core-taxprofiler_logo_custom_light.png
--- a/docs/images/nf-core-taxprofiler_logo_custom_light.svg
+++ b/docs/images/nf-core-taxprofiler_logo_custom_light.svg
--- a/docs/images/taxprofiler_logo.svg
+++ b/docs/images/taxprofiler_logo.svg
--- a/docs/usage.md
+++ b/docs/usage.md
@ -183,11 +183,11 @@ Complexity filtering can be activated via the `--perform_shortread_complexityfil

 Complexity filtering is primarily a run-time optimisation step. It is not necessary for accurate taxonomic profiling, however it can speed up run-time of each tool by removing reads with low-diversity of nucleotides (e.g. with mono-nucleotide - `AAAAAAAA`, or di-nucleotide repeats `GAGAGAGAGAGAGAG`) that have a low-chance of giving an informative taxonomic ID as they can be associated with many different taxa. Removing these reads therefore saves computational time and resources.

-There are currently two options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) and [`prinseq++`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/).
+There are currently three options for short-read complexity filtering: [`bbduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/), [`prinseq++`](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus), and [`fastp`](https://github.com/OpenGene/fastp#low-complexity-filter).

-The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of both tools (see links above) to decide on optimal methods and parameters for your dataset.
+The tools offer different algorithms and parameters for removing low complexity reads. We therefore recommend reviewing the pipeline's [parameter documentation](https://nf-co.re/taxprofiler/parameters) and the documentation of the tools (see links above) to decide on optimal methods and parameters for your dataset.

-You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`.
+You can optionally save the FASTQ output of the run merging with the `--save_complexityfiltered_reads`. If running with `fastp`, complexity filtering happens inclusively within the earlier shortread preprocessing step. Therefore there will not be an independent pipeline step for complexity filtering, and no independent FASTQ file (i.e. `--save_complexityfiltered_reads` will be ignored) - your complexity filtered reads will also be in the `fastp/` folder in the same file(s) as the preprocessed read.

 #### Host Removal

--- a/nextflow.config
+++ b/nextflow.config
@ -74,6 +74,7 @@ params {
    shortread_complexityfilter_bbduk_mask                = false
    shortread_complexityfilter_prinseqplusplus_mode      = 'entropy'
    shortread_complexityfilter_prinseqplusplus_dustscore = 0.5
+    shortread_complexityfilter_fastp_threshold           = 30
    save_complexityfiltered_reads                        = false

    // run merging
@ -131,11 +132,11 @@ try {

 // Load nf-core/taxprofiler custom profiles from different institutions.
 // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
-// }
+try {
+    includeConfig "${params.custom_config_base}/pipeline/taxprofiler.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/taxprofiler profiles: ${params.custom_config_base}/pipeline/taxprofiler.config")
+}


 profiles {
@ -187,6 +188,8 @@ profiles {
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
+    test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
+    test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
 }

 // Load igenomes.config if required
@ -225,7 +228,7 @@ trace {
 }
 dag {
    enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
+    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
 }

 manifest {
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@ -323,7 +323,8 @@
        },
        "shortread_complexityfilter_tool": {
            "type": "string",
-            "default": "bbduk"
+            "default": "bbduk",
+            "enum": ["bbduk", "prinseqplusplus", "fastp"]
        },
        "shortread_complexityfilter_bbduk_windowsize": {
            "type": "integer",
@ -427,6 +428,10 @@
            "type": "string",
            "default": "None"
        },
+        "shortread_complexityfilter_fastp_threshold": {
+            "type": "integer",
+            "default": 30
+        },
        "malt_save_reads": {
            "type": "boolean"
        },
--- a/subworkflows/local/shortread_complexityfiltering.nf
+++ b/subworkflows/local/shortread_complexityfiltering.nf
@ -13,6 +13,7 @@ workflow SHORTREAD_COMPLEXITYFILTERING {
    ch_versions       = Channel.empty()
    ch_multiqc_files  = Channel.empty()

+    // fastp complexity filtering is activated via modules.conf in shortread_preprocessing
    if ( params.shortread_complexityfilter_tool == 'bbduk' ) {
        ch_filtered_reads = BBMAP_BBDUK ( reads, [] ).reads
        ch_versions        =  ch_versions.mix( BBMAP_BBDUK.out.versions.first() )
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@ -19,9 +19,12 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input    ) { ch_input     = file(params.input)     } else { exit 1, 'Input samplesheet not specified!' }
 if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
+
 if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
 if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"

+if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_clipmerge == false || params.shortread_clipmerge_tool != 'fastp' ))  exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_clipmerge and/or --shortread_clipmerge_tool 'fastp'"
+
 if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
 if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }

@ -86,6 +89,7 @@ def multiqc_report = []
 workflow TAXPROFILER {

    ch_versions = Channel.empty()
+    ch_taxprofiler_logo = Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")

    /*
        SUBWORKFLOW: Read in samplesheet, validate and stage input files
@ -133,7 +137,8 @@ workflow TAXPROFILER {
        SUBWORKFLOW: COMPLEXITY FILTERING
    */

-    if ( params.perform_shortread_complexityfilter ) {
+    // fastp complexity filtering is activated via modules.conf in shortread_preprocessing
+    if ( params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp' ) {
        ch_shortreads_filtered = SHORTREAD_COMPLEXITYFILTERING ( ch_shortreads_preprocessed ).reads
        ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
    } else {
@ -222,6 +227,8 @@ workflow TAXPROFILER {
    ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))

+    ch_multiqc_files = ch_multiqc_files.mix(ch_taxprofiler_logo.ifEmpty([]))
+
    if (params.perform_shortread_clipmerge) {
        ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
    }
@ -230,7 +237,7 @@ workflow TAXPROFILER {
        ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
    }

-    if (params.perform_shortread_complexityfilter){
+    if (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool != 'fastp'){
        ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_COMPLEXITYFILTERING.out.mqc.collect{it[1]}.ifEmpty([]) )
    }