update to version 2.0.0

CHANGELOG.md

@@ -3,6 +3,16 @@
 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).
 
+## v2.0.0 - [04/11/24]
+
+- Significant recoding of pipeline to bring it more in line with current nf-core template.
+- Add Krona to produce graphical outputs of Bracken results. Path to Krona Taxonomy file will have to be specified with `--kronadb`.
+- Update FastQC from version 0.11.9 to version 0.12.1.
+- Update fastp from version 0.23.2 to version 0.23.4.
+- Update Kraken 2 from version 2.1.2 to version 2.1.3.
+- Update Bracken from version 2.7 to version 2.9.
+- Update MultiQC from version 1.13 to version 1.25.1. Report now includes Bracken outputs instead of Kraken 2 outputs.
+
 ## v1.2 - [30/01/24]
 
 - Remove `--brackendb` parameter as redundant. Bracken will now use the database location specified with `--krakendb`.

CITATIONS.md

@@ -23,6 +23,9 @@
 - [Kraken 2](https://www.ncbi.nlm.nih.gov/pubmed/31779668/)
     > Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019 Nov 28;20(1):257. doi: 10.1186/s13059-019-1891-0. PubMed PMID: 31779668; PubMed Central PMCID: PMC6883579.
 
+- [Krona](https://pubmed.ncbi.nlm.nih.gov/21961884/)
+    > Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385. PMID: 21961884; PMCID: PMC3190407.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 

assets/methods_description_template.yml

@@ -0,0 +1,27 @@
+id: "avantonder-bacQC-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "avantonder/bacQC Methods Description"
+section_href: "https://github.com/avantonder/bacQC"
+plot_type: "html"
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using avantonder/bacQC v${workflow.manifest.version} ${doi_text} utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>The pipeline was executed with Nextflow v${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>
+  <h4>References</h4>
+  <ul>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The avantonder framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
+  </ul>
+  <div class="alert alert-info">
+    <h5>Notes:</h5>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>

assets/multiqc_config.yml

@@ -1,37 +1,98 @@
 report_comment: >
     This report has been generated by the <a href="https://github.com/avantonder/bacQC" target="_blank">bacQC</a>
     analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/avantonder/bacQC" target="_blank">documentation</a>.
+    <a href="https://github.com/avantonder/bacQC/blob/main/docs/output.md" target="_blank">documentation</a>.
 
-data_format: "yaml"
 
-max_table_rows: 10000
+report_section_order:
+  "avantonder-bacQC-methods-description":
+    order: -1000
+  software_versions:
+    order: -1001
+  "avantonder-bacqc-summary":
+    order: -1002
+  general_stats":
+    order: 1000
+  fastqc:
+    order: 900
+  fastp:
+    order: 800
+  kraken:
+    order: 700
+  bracken:
+    order: 600
+
+export_plots: true
 
 run_modules:
-  - custom_content
   - fastqc
   - fastp
   - kraken
+  - custom_content
 
-module_order:
-  - fastqc:
-      name: "PREPROCESS: FastQC (raw reads)"
+top_modules:
+  - "fastqc":
+      name: "FastQC (raw reads)"
       info: "This section of the report shows FastQC results for the raw reads before adapter trimming."
       path_filters:
-        - "./fastqc/*.zip"
-  - fastp:
-      name: "PREPROCESS: fastp (adapter trimming)"
+        - "*_fastqc.zip"
+  - "fastp":
+      name: "fastp (adapter trimming)"
       info: "This section of the report shows fastp results for reads after adapter and quality trimming."
-  - kraken:
-      name: "PREPROCESS: Kraken 2"
-      info: "This section of the report shows Kraken 2 classification results for reads after adapter trimming with fastp."
+  - "kraken":
+      name: "Kraken"
+      path_filters:
+        - "*.kraken2.kraken2.report.txt"
+  - "kraken":
+      name: "Bracken"
+      anchor: "bracken"
+      target: "Bracken"
+      doi: "10.7717/peerj-cs.104"
+      info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
+      extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
+      path_filters:
+        - "*.bracken.kraken2.report.txt"
 
-report_section_order:
-  summary_assembly_metrics:
-    before: summary_variants_metrics
-  software_versions:
-    order: -1001
-  "nf-core-bacqc-summary":
-    order: -1002
+table_columns_placement:
+  FastQC (raw reads):
+    total_sequences: 100
+    avg_sequence_length: 110
+    median_sequence_length: 120
+    percent_duplicates: 130
+    percent_gc: 140
+    percent_fails: 150
+  fastp (adapter trimming):
+    pct_adapter: 300
+    pct_surviving: 310
+    pct_duplication: 320
+    after_filtering_gc_content: 330
+    after_filtering_q30_rate: 340
+    after_filtering_q30_bases: 350
+    filtering_result_passed_filter_reads: 360
+  Bracken:
+    "% Unclassified": 1200
+    "% Top 5": 1210
+  Kraken:
+    "% Unclassified": 1600
+    "% Top 5": 1610
+
+table_columns_visible:
+  FastQC (raw reads):
+    total_sequences: True
+    avg_sequence_length: True
+    percent_duplicates: True
+    percent_gc: True
+    percent_fails: False
+  Kraken: False
+  Bracken: False
+
+table_columns_name:
+  FastQC (raw reads):
+    total_sequences: "Nr. Input Reads"
+    avg_sequence_length: "Length Input Reads"
+    percent_gc: "% GC Input Reads"
+    percent_duplicates: "% Dups Input Reads"
+    percent_fails: "% Failed Input Reads"
 
-export_plots: true
+section_comments:
+  general_stats: "By default, all read count columns are displayed as millions (M) of reads."

assets/sendmail_template.txt

@@ -9,21 +9,21 @@ Content-Type: text/html; charset=utf-8
 $email_html
 
 --nfcoremimeboundary
-Content-Type: image/png;name="nf-core-bacqc_logo.png"
+Content-Type: image/png;name="bacqc_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="nf-core-bacqc_logo.png"
+Content-Disposition: inline; filename="bacqc_logo.png"
 
-<% out << new File("$projectDir/assets/nf-core-bacqc_logo.png").
-  bytes.
-  encodeBase64().
-  toString().
-  tokenize( '\n' )*.
-  toList()*.
-  collate( 76 )*.
-  collect { it.join() }.
-  flatten().
-  join( '\n' ) %>
+<% out << new File("$projectDir/assets/bacqc_logo.png").
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' ) %>
 
 <%
 if (mqcFile){
@@ -37,17 +37,17 @@ Content-ID: <mqcreport>
 Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
 
 ${mqcFileObj.
-  bytes.
-  encodeBase64().
-  toString().
-  tokenize( '\n' )*.
-  toList()*.
-  collate( 76 )*.
-  collect { it.join() }.
-  flatten().
-  join( '\n' )}
+    bytes.
+    encodeBase64().
+    toString().
+    tokenize( '\n' )*.
+    toList()*.
+    collate( 76 )*.
+    collect { it.join() }.
+    flatten().
+    join( '\n' )}
 """
 }}
 %>
 
---nfcoremimeboundary--
+--nfcoremimeboundary--