docs: Add analysis example

docs/analysis_example.md

@@ -0,0 +1,94 @@
+# Example analysis - Crohn's disease microbiome data
+
+To showcase the potential EURYALE has to expedite the analysis of microbiome data, let's
+try analysing a publicly available gut microbiome dataset ([PRJNA175224](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA175224)).
+This dataset contains 7 gut microbiome samples from healthy donors and 4 from donors with Crohn's disease.
+
+Feel free to download the original dataset to a directory called `raw_data` and follow along.
+
+## Acquiring databases and running the pipeline
+
+Let's first download the databases and references.
+For this analysis, we'll focus on the taxonomic classification results after de-contamination.
+So, let's download the Human reference genome as well as Kaiju's database:
+
+```bash
+nextflow run dalmolingroup/euryale \
+  --download_kaiju \
+  --download_host \
+  --outdir references \
+  -entry download \
+  -profile singularity
+```
+
+Once that's done, let's execute the analysis on the data itself.
+Your samplesheet should look something like this:
+
+```csv
+sample,fastq_1,fastq_2
+SRR579274,raw_data/SRR579274_1.fastq.gz,raw_data/SRR579274_2.fastq.gz
+SRR579275,raw_data/SRR579275_1.fastq.gz,raw_data/SRR579275_2.fastq.gz
+SRR579276,raw_data/SRR579276_1.fastq.gz,raw_data/SRR579276_2.fastq.gz
+SRR579277,raw_data/SRR579277_1.fastq.gz,raw_data/SRR579277_2.fastq.gz
+SRR579278,raw_data/SRR579278_1.fastq.gz,raw_data/SRR579278_2.fastq.gz
+SRR579279,raw_data/SRR579279_1.fastq.gz,raw_data/SRR579279_2.fastq.gz
+SRR579280,raw_data/SRR579280_1.fastq.gz,raw_data/SRR579280_2.fastq.gz
+SRR579281,raw_data/SRR579281_1.fastq.gz,raw_data/SRR579281_2.fastq.gz
+SRR579290,raw_data/SRR579290_1.fastq.gz,raw_data/SRR579290_2.fastq.gz
+SRR579291,raw_data/SRR579291_1.fastq.gz,raw_data/SRR579291_2.fastq.gz
+SRR579292,raw_data/SRR579292_1.fastq.gz,raw_data/SRR579292_2.fastq.gz
+```
+
+And your command should look something like this one:
+
+```bash
+nextflow run dalmolingroup/euryale \
+          --input samplesheet.csv \
+          --outdir results \
+          --skip_alignment \
+          --skip_functional \
+          --kaiju_db references/kaiju_db_nr_2023-05-10.tgz \
+          --host_fasta references/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
+          -profile singularity \
+          -r "v1.0.3"
+```
+
+Check the [parameter documentation](https://dalmolingroup.github.io/euryale/params/) for a full description
+of possible parameters.
+
+- We're skipping the functional annotation section just to expedite the results, but feel free to include these
+  steps in your own analysis.
+
+Once that's all done, let's check the results we got.
+
+## Exploring the resulting data
+
+First, let's open the MultiQC report in our browser and take a look.
+It should be available in `results/multiqc/multiqc_report.html`.
+
+We can first see that most reads (80%) in each sample passed
+the quality filter, thankfully:
+
+![](assets/fastp_filtered_reads_plot.png)
+
+We can also see that most samples did not have their reads assigned
+to any particular taxon:
+
+![](assets/kaiju-topfive-plot.png)
+
+This could be due to high host contamination, or could necessitate
+the use of another database, or something else entirely! Either way, it's something worth investigating.
+We can also see there is a strange spike of _Enterocloster boltae_ in one of the samples, which also
+warrants further investigation.
+
+If we now check the MicroView results, available in `results/taxonomy/microview/microview_report.html`,
+we can see further points of interest to investigate in our data.
+
+Let's see the Beta-diversity PCoA, for example:
+
+![](assets/betadiv_microview.png)
+
+The plot shows a somewhat strange division in the dataset: 4 samples stretch further in
+the PC1 than the rest. This could be due to some biological variable or an error in the data generation process.
+Either way, it's worth saving the PCoA table, available in `results/taxonomy/microview/microview_tables/` and
+crossing the sample names with the metadata of this study.

mkdocs.yml

@@ -5,6 +5,7 @@ nav:
   - Home: README.md
   - Usage: usage.md
   - Output: output.md
+  - Analysis Example: analysis_example.md
   - Citations: CITATIONS.md
   - Reference:
       - Parameters: params.md