From aa01844ac350f5e7279b95ccd945738bcea2a789 Mon Sep 17 00:00:00 2001
From: Xichen Wu <xichenwu@outlook.com>
Date: Mon, 6 Nov 2023 19:35:18 +0100
Subject: [PATCH] add quick starts for three mode

---
 docs/source/genetic.md |  7 +++++++
 docs/source/hashing.md |  7 +++++++
 docs/source/index.md   | 11 ++++++-----
 docs/source/rescue.md  |  7 +++++++
 4 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/docs/source/genetic.md b/docs/source/genetic.md
index 66b5abd..aafb2bc 100644
--- a/docs/source/genetic.md
+++ b/docs/source/genetic.md
@@ -6,6 +6,13 @@ Genotyped-based deconvolution leverages the unique genetic composition of indivi
 
 ![Caption](_static/images/genotype-based.png)
 
+## **Quick start**
+
+```bash
+cd hadge
+nextflow run main.nf -profile test --mode genetic
+```
+
 ## **Input data preparation**
 
 The input data depends heavily on the deconvolution tools. In the following table, you will find the minimal input data required by different tools.
diff --git a/docs/source/hashing.md b/docs/source/hashing.md
index 5a1a305..c849bfb 100644
--- a/docs/source/hashing.md
+++ b/docs/source/hashing.md
@@ -6,6 +6,13 @@ Cell hashing is a sample processing technique that requires processing individua
 
 ![Caption](_static/images/hashing-based.png)
 
+## **Quick start**
+
+```bash
+cd hadge
+nextflow run main.nf -profile test --mode hashing
+```
+
 ## **Input data preparation**
 
 The input data depends heavily on the deconvolution tools. In the following table, you will find the minimal input data required by different tools.
diff --git a/docs/source/index.md b/docs/source/index.md
index 2004ea5..fb0656e 100644
--- a/docs/source/index.md
+++ b/docs/source/index.md
@@ -43,11 +43,13 @@ You can also:
 - Specify the folder name `--outdir` to save the output files. This will create a folder automatically in the project directory.
 - Specify the input data for each process.
 - The pipeline can be run either locally or on a HPC with different resource specifications. As default, the pipeline will run locally. You can also set the SLURM executor by running the pipeline with `-profile cluster`.
-- Please also check [](usage) for more details.
+- Please also check [](general) for more details.
 
 ## **Quick start**
 
 ```bash
+git clone https://github.com/theislab/hadge.git
+cd hadge
 sh test_data/download_data.sh
 nextflow run main.nf -profile test
 ```
@@ -69,7 +71,7 @@ If the pipeline is run on single sample, each demultiplexing process will genera
 If the pipeline is run on multiple samples, the `task_ID` will be replaced by `sampleId`. In the folder, you can find following files:
 
 - `params.csv`: specified parameters in the task
-- Output of the task, check [](output) for more details.
+- Output of the task, check [](genetic) and [](hashing) for more details.
 
 ### **Final output**
 
@@ -86,17 +88,16 @@ After each demultiplexing workflow is complete, the pipeline will generate TSV f
 
 Before running the donor-matching preocess, the pipeline merges the results of hashing and genetic demultiplexing tools into `classification_all_genetic_and_hash.csv` and `assignment_all_genetic_and_hash.csv` in the `$pipeline_output_folder/summary` folder.
 
-The output of the donor-matching process can be found in the folder `donor_match`, check [](output) for more details.
+The output of the donor-matching process can be found in the folder `donor_match`, check [](rescue) for more details.
 
 ```{toctree}
 :caption: 'Contents:'
 :hidden: true
 :maxdepth: 3
-usage
-output
 general
 genetic
 hashing
+rescue
 ```
 
 # Indices and tables
diff --git a/docs/source/rescue.md b/docs/source/rescue.md
index 1a5a5b3..76bd6d2 100644
--- a/docs/source/rescue.md
+++ b/docs/source/rescue.md
@@ -6,6 +6,13 @@ The joint call of hashing and genetic deconvolution methods has been shown to be
 
 ![Caption](_static/images/rescue.png)
 
+## **Quick start**
+
+```bash
+cd hadge
+nextflow run main.nf -profile test
+```
+
 ## **Parameter**
 
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