Add kraken2 phylogenetic assignment subworkflow

CHANGELOG.md

@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#47](https://github.com/nf-core/seqinspector/pull/47) Added kraken2 subworkflow
 - [#50](https://github.com/nf-core/seqinspector/pull/50) Add an optional subsampling step.
 - [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 - [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools

CITATIONS.md

@@ -14,6 +14,14 @@
 
 > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
+
+  > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0
+
+- [Krona](https://doi.org/10.1186/1471-2105-12-385)
+
+  > Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12. https://doi.org/10.1186/1471-2105-12-385
+
 - [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.

conf/modules.config

@@ -26,6 +26,40 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: 'KRAKEN2_KRAKEN2' {
+        publishDir = [
+            path: { "${params.outdir}/kraken2_reports" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'KRONA_KTUPDATETAXONOMY' {
+        publishDir = [
+            path: { "${params.outdir}/kraken2_reports/krona_reports" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: false
+        ]
+    }
+
+    withName: 'KRONA_KTIMPORTTAXONOMY' {
+        publishDir = [
+            path: { "${params.outdir}/kraken2_reports/krona_reports" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'UNTAR' {
+        publishDir = [
+            path: { "${params.outdir}/kraken2_db" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_uncompressed_k2db
+        ]
+    }
+
     withName: 'MULTIQC_GLOBAL' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

conf/test.config

@@ -29,4 +29,8 @@ params {
 
     // Genome references
     genome = 'R64-1-1'
+
+    // Kraken options
+    // Database information:  https://github.com/nf-core/test-datasets/blob/taxprofiler/README.md#kraken2
+    kraken2_db = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz'
 }

conf/test_full.config

@@ -21,4 +21,8 @@ params {
 
     // Genome references
     genome = 'R64-1-1'
+
+    // Kraken
+    // Database information: https://github.com/nf-core/test-datasets/blob/taxprofiler/README.md#kraken2
+    kraken2_db  = 'https://github.com/nf-core/test-datasets/raw/taxprofiler/data/database/kraken2/testdb-kraken2.tar.gz'
 }

docs/output.md

@@ -12,6 +12,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [Seqtk](#seqtk) - Subsample a specific number of reads per sample
 - [FastQC](#fastqc) - Raw read QC
+- [Kraken2](#kraken2) - Phylogenetic assignment of reads using k-mers
+- [Krona](#krona) - Interactive visualization of Kraken2 results
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -40,6 +42,41 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
 
+### Kraken2
+
+[Kraken](https://ccb.jhu.edu/software/kraken2/) is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps -mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `kraken2/`
+  - `<sample>.kraken2.report.txt`: A report containing information on the phylogenetic assignment of reads in a given sample.
+  - `<db_name>/`
+    - `<sample_id>_<db_name>.classified.fastq.gz`: FASTQ file containing all reads that had a hit against a reference in the database for a given sample
+    - `<sample_id>_<db_name>.unclassified.fastq.gz`: FASTQ file containing all reads that did not have a hit in the database for a given sample
+    - `<sample_id>_<db_name>.classifiedreads.txt`: A list of read IDs and the hits each read had against each database for a given sample
+
+</details>
+
+The main taxonomic classification file from Kraken2 is the `*report.txt` file. It gives you the most information for a single sample.
+You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply `--kraken2_save_reads` and/or `--kraken2_save_readclassifications` parameters to the pipeline.
+
+### Krona
+
+[Krona](https://github.com/marbl/Krona) allows the exploration of (metagenomic) hierarchical data with interactive zooming, multi-layered pie charts.
+
+Krona charts will be generated by the pipeline for supported tools (Kraken2, Centrifuge, Kaiju, and MALT)
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `krona/`
+  - `<tool_name>_<db_name>.html`: per-tool/per-database interactive HTML file containing hierarchical piecharts
+
+</details>
+
+The resulting HTML files can be loaded into your web browser for exploration. Each file will have a dropdown to allow you to switch between each sample aligned against the given database of the tool.
+
 ### MultiQC
 
 nf-core/seqinspector will generate the following MultiQC reports:

modules.json

@@ -10,11 +10,31 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "kraken2/kraken2": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/ktimporttaxonomy": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/ktupdatetaxonomy": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "seqtk/sample": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",