From e7099ae415902dd8c73ad808f15e8c681d1d8a61 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@kuleuven.be>
Date: Mon, 3 Jun 2024 09:33:50 +0000
Subject: [PATCH] A quickstart is made

---
 docs/quickstart.md | 82 ++++++++++++++++++++++++++++++++++++++++++++++
 mkdocs.yml         |  1 +
 2 files changed, 83 insertions(+)
 create mode 100644 docs/quickstart.md

diff --git a/docs/quickstart.md b/docs/quickstart.md
new file mode 100644
index 0000000..cac2e54
--- /dev/null
+++ b/docs/quickstart.md
@@ -0,0 +1,82 @@
+# Quick Start
+
+Viralgenie needs two things:
+
+ 1. [Nextflow](https://www.nextflow.io/)
+ 2. [Docker](https://www.docker.com/resources/what-container/) - [Singularity](https://docs.sylabs.io/guides/latest/user-guide/introduction.html) - [Conda](https://docs.conda.io/en/latest/)
+
+```bash
+# Install nextflow with conda
+conda install nextflow
+```
+
+Run the pipeline with a small test dataset with docker containers:
+```bash
+nextflow run Joon-Klaps/viralgenie \
+    -profile test,docker
+```
+
+> For a more complete guide on how to set up Nextflow, Docker, Singularity, and Conda, see the [installation guide](installation.md).
+
+## Running viralgenie with your own samples
+
+```bash
+nextflow run Joon-Klaps/viralgenie \
+    -profile test,docker \
+    --input my_samplesheet.csv
+```
+
+An input file contains the paths to the fastq files and the sample names. The input file can be in TSV, CSV, YAML, or JSON format.
+
+=== "TSV"
+
+    ```tsv title="input-samplesheet.tsv"
+    sample	fastq_1	fastq_2
+    sample1	AEG588A1_S1_L002_R1_001.fastq.gz	AEG588A1_S1_L002_R2_001.fastq.gz
+    sample2	AEG588A5_S5_L003_R1_001.fastq.gz
+    sample3	AEG588A3_S3_L002_R1_001.fastq.gz	AEG588A3_S3_L002_R2_001.fastq.gz
+    ```
+
+=== "CSV"
+
+    ```csv title="input-samplesheet.csv"
+    sample,fastq_1,fastq_2
+    sample1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+    sample2,AEG588A5_S5_L003_R1_001.fastq.gz,
+    sample3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz
+    ```
+
+
+=== "YAML"
+
+    ```yaml title="input-samplesheet.yaml"
+    - sample: sample1
+    fastq1: AEG588A1_S1_L002_R1_001.fastq.gz
+    fastq2: AEG588A1_S1_L002_R2_001.fastq.gz
+    - sample: sample2
+    fastq1: AEG588A5_S5_L003_R1_001.fastq.gz
+    - sample: sample3
+    fastq1: AEG588A3_S3_L002_R1_001.fastq.gz
+    fastq2: AEG588A3_S3_L002_R2_001.fastq.gz
+    ```
+
+=== "JSON"
+    ```json title="samplesheet.json"
+    [
+        {
+            "sample": "sample1",
+            "fastq1": "AEG588A1_S1_L002_R1_001.fastq.gz",
+            "fastq2": "AEG588A1_S1_L002_R2_001.fastq.gz",
+        },
+        {
+            "sample": "sample2",
+            "fastq1": "AEG588A5_S5_L003_R1_001.fastq.gz",
+        },
+        {
+            "sample": "sample3",
+            "fastq1": "AEG588A3_S3_L002_R1_001.fastq.gz",
+            "fastq2": "AEG588A3_S3_L002_R2_001.fastq.gz",
+        }
+    ]
+    ```
+
diff --git a/mkdocs.yml b/mkdocs.yml
index 4561f0f..a005ab7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -10,6 +10,7 @@ nav:
       - "Usage": usage.md
       - "Output": output.md
       - "Citations": CITATIONS.md
+  - Quick Start: quickstart.md
   - Workflow:
       - "Pipeline overview": workflow/overview.md
       - "Preprocessing": workflow/preprocessing.md