Implementation of KmerFinder subworkflow Custom Quast, and Custom MultiQC Reports

CHANGELOG.md

@@ -7,8 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#135](https://github.com/nf-core/bacass/pull/135) Replaced nf-core MultiQC module with a custom MultiQC module.
+
 ### `Added`
 
+- [#135](https://github.com/nf-core/bacass/pull/135) Implementation of KmerFinder subworkflow Custom Quast, and Custom MultiQC Reports:
+
+  - Added KmerFinder subworkflow for read quality control, purity assessment, and sample grouping based on reference genome estimation.
+  - Enhanced Quast Assembly QC to run both general and reference genome-based analyses when KmerFinder is invoked.
+  - Implemented custom MultiQC module with multiqc_config.yml files for different assembly modes (short, long, hybrid).
+  - Generated custom MultiQC HTML report consolidating metrics from KmerFinder, Quast, and other relevant sources.
+
 - [#133](https://github.com/nf-core/bacass/pull/133) Update nf-core/bacass to the new nf-core 2.14.1 `TEMPLATE`.
 
 ### `Fixed`

README.md

@@ -29,11 +29,12 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ### Short Read Assembly
 
-This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [FastP](https://github.com/OpenGene/fastp) and performs basic sequencing QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) to verify sample purity.
+This pipeline is primarily for bacterial assembly of next-generation sequencing reads. It can be used to quality trim your reads using [FastP](https://github.com/OpenGene/fastp) and performs basic sequencing QC using [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, the pipeline performs read assembly using [Unicycler](https://github.com/rrwick/Unicycler). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) and [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) to verify sample purity.
 
 ### Long Read Assembly
 
-For users that only have Nanopore data, the pipeline quality trims these using [PoreChop](https://github.com/rrwick/Porechop) and assesses basic sequencing QC utilizing [NanoPlot](https://github.com/wdecoster/NanoPlot) and [PycoQC](https://github.com/a-slide/pycoQC).
+For users that only have Nanopore data, the pipeline quality trims these using [PoreChop](https://github.com/rrwick/Porechop) and assesses basic sequencing QC utilizing [NanoPlot](https://github.com/wdecoster/NanoPlot) and [PycoQC](https://github.com/a-slide/pycoQC). Contamination of the assembly is checked using [Kraken2](https://ccb.jhu.edu/software/kraken2/) and [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) to verify sample purity.
+
 The pipeline can then perform long read assembly utilizing [Unicycler](https://github.com/rrwick/Unicycler), [Miniasm](https://github.com/lh3/miniasm) in combination with [Racon](https://github.com/isovic/racon), [Canu](https://github.com/marbl/canu) or [Flye](https://github.com/fenderglass/Flye) by using the [Dragonflye](https://github.com/rpetit3/dragonflye)(\*) pipeline. Long reads assembly can be polished using [Medaka](https://github.com/nanoporetech/medaka) or [NanoPolish](https://github.com/jts/nanopolish) with Fast5 files.
 
 > [!NOTE]
@@ -47,6 +48,10 @@ For users specifying both short read and long read (NanoPore) data, the pipeline
 
 In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quast). The resulting bacterial assembly is furthermore annotated using [Prokka](https://github.com/tseemann/prokka), [Bakta](https://github.com/oschwengers/bakta) or [DFAST](https://github.com/nigyta/dfast_core).
 
+If Kmerfinder is invoked, the pipeline will group samples according to the [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)-estimated reference genomes. Afterwards, two QUAST steps will be carried out: an initial ('general') [QUAST](http://bioinf.spbau.ru/quast) of all samples without reference genomes, and subsequently, a 'by reference genome' [QUAST](http://bioinf.spbau.ru/quast) to aggregate samples with their reference genomes.
+
+> NOTE: This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only.
+
 ## Usage
 
 > [!NOTE]

assets/multiqc_config_hybrid.yml

@@ -0,0 +1,166 @@
+report_comment: >
+  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/dev" target="_blank">nf-core/bacass</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
+
+data_format: "yaml"
+
+max_table_rows: 10000
+
+run_modules:
+  - custom_content
+  - fastqc
+  - fastp
+  - nanostat
+  - porechop
+  - pycoqc
+  - kraken2
+  - quast
+  - prokka
+  - bakta
+
+exclude_modules:
+  - general_stats
+
+module_order:
+  - fastqc:
+      name: "PREPROCESS: 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)"
+      info: "This section of the report shows fastp results for reads after adapter and quality trimming."
+      path_filters:
+        - "./fastp/*.json"
+  - nanostat:
+      name: "PREPROCESS: Nanoplot"
+      info: "This section of the report shows Nanoplot results for nanopore sequencing data."
+      path_filters:
+        - "./nanoplot/*.txt"
+  - porechop:
+      name: "PREPROCESS: Porechop"
+      info: "This section of the report shows Porechop results for reads after adapter trimming."
+      path_filters:
+        - "./porechop/*.log"
+  - pycoqc:
+      name: "PREPROCESS: PycoQC"
+      info: "This section of the report shows PycoQC results for quality control of long-read sequencing data."
+      path_filters:
+        - "./pycoqc/*.txt"
+  - kraken2:
+      name: "CONTAMINATION ANALYSIS: Kraken 2"
+      info: "This section of the report shows Kraken 2 classification results for reads after adapter trimming with fastp."
+      path_filters:
+        - ".*kraken2_*/*report.txt"
+  - quast:
+      name: "ASSEMBLY: Quast"
+      info: "This section of the report shows Quast QC results for assembled genomes with Unicycler."
+      path_filters:
+        - "./quast/*/report.tsv"
+  - prokka:
+      name: "ANNOTATION: Prokka"
+      info: "This section of the report shows Prokka annotation results for reads after adapter trimming and quality trimming."
+      path_filters:
+        - "./prokka/*.txt"
+  - bakta:
+      name: "ANNOTATION: Bakta"
+      info: "This section of the report shows Bakta mapping and annotation results for reads after adapter trimming."
+      path_filters:
+        - "./bakta/*.txt"
+
+report_section_order:
+  fastqc:
+    after: general_stats
+  fastp:
+    after: general_stats
+  nanostat:
+    after: general_stats
+  porechop:
+    before: nanostat
+  kraken2:
+    after: general_stats
+  quast:
+    after: general_stats
+  prokka:
+    before: nf-core-bacass-methods-description
+  bakta:
+    before: nf-core-bacass-methods-description
+  nf-core-bacass-methods-description:
+    order: -1000
+  software_versions:
+    order: -1001
+  nf-core-bacass-summary:
+    order: -1002
+
+custom_data:
+  summary_assembly_metrics:
+    section_name: "De novo assembly metrics (shorts & long reads)"
+    description: "generated by nf-core/bacass"
+    plot_type: "table"
+    headers:
+      "Sample":
+        description: "Input sample names"
+        format: "{:,.0f}"
+      "# Input short reads":
+        description: "Total number of input reads in raw fastq files"
+        format: "{:,.0f}"
+      "# Trimmed short reads (fastp)":
+        description: "Total number of reads remaining after adapter/quality trimming with fastp"
+        format: "{:,.0f}"
+      "# Input long reads":
+        description: "Total number of input reads in raw fastq files"
+        format: "{:,.0f}"
+      "# Median long reads lenght":
+        description: "Median read lenght (bp)"
+        format: "{:,.0f}"
+      "# Median long reads quality":
+        description: "Median read quality (Phred scale)"
+        format: "{:,.0f}"
+      "# Contigs (hybrid assembly)":
+        description: "Total number of contigs calculated by QUAST"
+        format: "{:,.0f}"
+      "# Largest contig (hybrid assembly)":
+        description: "Size of largest contig calculated by QUAST"
+        format: "{:,.0f}"
+      "# N50 (hybrid assembly)":
+        description: "N50 metric for de novo assembly as calculated by QUAST"
+        format: "{:,.0f}"
+      "# % Genome fraction (hybrid assembly)":
+        description: "% genome fraction calculated by QUAST"
+        format: "{:,.2f}"
+      "# Best hit (Kmerfinder)":
+        description: "Specie name of the best hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Best hit assembly ID (Kmerfinder)":
+        description: "Assembly ID of the best hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Best hit query coverage (Kmerfinder)":
+        description: "Query coverage value of the best hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Best hit depth (Kmerfinder)":
+        description: "Depth of the best hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Second hit (Kmerfinder)":
+        description: "Specie name of the second hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Second hit assembly ID (Kmerfinder)":
+        description: "Assembly ID of the second hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Second hit query coverage (Kmerfinder)":
+        description: "Query coverage value of the second hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+      "# Second hit depth (Kmerfinder)":
+        description: "Depth of the second hit from Kmerfinder (using short reads)"
+        format: "{:,.0f}"
+
+export_plots: true
+
+# # Customise the module search patterns to speed up execution time
+# #  - Skip module sub-tools that we are not interested in
+# #  - Replace file-content searching with filename pattern searching
+# #  - Don't add anything that is the same as the MultiQC default
+# # See https://multiqc.info/docs/#optimise-file-search-patterns for details
+sp:
+  fastp:
+    fn: "*.fastp.json"

assets/multiqc_config_long.yml

@@ -0,0 +1,140 @@
+report_comment: >
+  This report has been generated by the <a href="https://github.com/nf-core/bacass/releases/tag/dev" target="_blank">nf-core/bacass</a>
+  analysis pipeline. For information about how to interpret these results, please see the
+  <a href="https://nf-co.re/bacass/dev/docs/output" target="_blank">documentation</a>.
+
+data_format: "yaml"
+
+max_table_rows: 10000
+
+run_modules:
+  - custom_content
+  - nanostat
+  - porechop
+  - pycoqc
+  - kraken2
+  - quast
+  - prokka
+  - bakta
+
+exclude_modules:
+  - general_stats
+
+module_order:
+  - nanostat:
+      name: "PREPROCESS: Nanoplot"
+      info: "This section of the report shows Nanoplot results for nanopore sequencing data."
+      path_filters:
+        - "./nanoplot/*.txt"
+  - porechop:
+      name: "PREPROCESS: Porechop"
+      info: "This section of the report shows Porechop results for reads after adapter trimming."
+      path_filters:
+        - "./porechop/*.log"
+  - pycoqc:
+      name: "PREPROCESS: PycoQC"
+      info: "This section of the report shows PycoQC results for quality control of long-read sequencing data."
+      path_filters:
+        - "./pycoqc/*.txt"
+  - kraken2:
+      name: "CONTAMINATION ANALYSIS: Kraken 2"
+      info: "This section of the report shows Kraken 2 classification results for reads after adapter trimming with fastp."
+      path_filters:
+        - ".*kraken2_*/*report.txt"
+  - quast:
+      name: "ASSEMBLY: Quast"
+      info: "This section of the report shows Quast QC results for assembled genomes with Unicycler."
+      path_filters:
+        - "./quast/*/report.tsv"
+  - prokka:
+      name: "ANNOTATION: Prokka"
+      info: "This section of the report shows Prokka annotation results for reads after adapter trimming and quality trimming."
+      path_filters:
+        - "./prokka/*.txt"
+  - bakta:
+      name: "ANNOTATION: Bakta"
+      info: "This section of the report shows Bakta mapping and annotation results for reads after adapter trimming."
+      path_filters:
+        - "./bakta/*.txt"
+
+report_section_order:
+  nanostat:
+    after: general_stats
+  porechop:
+    before: nanostat
+  kraken2:
+    after: general_stats
+  quast:
+    after: general_stats
+  prokka:
+    before: nf-core-bacass-methods-description
+  bakta:
+    before: nf-core-bacass-methods-description
+  nf-core-bacass-methods-description:
+    order: -1000
+  software_versions:
+    order: -1001
+  nf-core-bacass-summary:
+    order: -1002
+
+custom_data:
+  summary_assembly_metrics:
+    section_name: "De novo assembly metrics (long-reads)"
+    description: "generated by nf-core/bacass"
+    plot_type: "table"
+    headers:
+      "Sample":
+        description: "Input sample names"
+        format: "{:,.0f}"
+      "# Input reads":
+        description: "Total number of input reads in raw fastq files"
+        format: "{:,.0f}"
+      "# Median read lenght":
+        description: "Median read lenght (bp)"
+        format: "{:,.0f}"
+      "# Median read quality":
+        description: "Median read quality (Phred scale)"
+        format: "{:,.0f}"
+      "# Contigs":
+        description: "Total number of contigs calculated by QUAST"
+        format: "{:,.0f}"
+      "# Largest contig":
+        description: "Size of largest contig calculated by QUAST"
+        format: "{:,.0f}"
+      "# N50":
+        description: "N50 metric for de novo assembly as calculated by QUAST"
+        format: "{:,.0f}"
+      "# % Genome fraction":
+        description: "% genome fraction calculated by QUAST"
+        format: "{:,.2f}"
+      "# Best hit (Kmerfinder)":
+        description: "Specie name of the best hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Best hit assembly ID (Kmerfinder)":
+        description: "Assembly ID of the best hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Best hit query coverage (Kmerfinder)":
+        description: "Query coverage value of the best hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Best hit depth (Kmerfinder)":
+        description: "Depth of the best hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Second hit (Kmerfinder)":
+        description: "Specie name of the second hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Second hit assembly ID (Kmerfinder)":
+        description: "Assembly ID of the second hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Second hit query coverage (Kmerfinder)":
+        description: "Query coverage value of the second hit from Kmerfinder"
+        format: "{:,.0f}"
+      "# Second hit depth (Kmerfinder)":
+        description: "Depth of the second hit from Kmerfinder"
+        format: "{:,.0f}"
+
+export_plots: true
+# # Customise the module search patterns to speed up execution time
+# #  - Skip module sub-tools that we are not interested in
+# #  - Replace file-content searching with filename pattern searching
+# #  - Don't add anything that is the same as the MultiQC default
+# # See https://multiqc.info/docs/#optimise-file-search-patterns for details