Merge branch 'main' of https://github.com/SFGLab/hichip-nf-pipeline i…

…nto main

README.md

@@ -1,19 +1,34 @@
-# nf-HiChIP pipeline
-Pipeline for processing HiChIP data.
+<h2 align="center"> nf-HiChIP Pipeline </h2>
 
-Docker image available: https://hub.docker.com/repository/docker/mateuszchilinski/hichip-nf-pipeline/general
+<p align="center">
+<img align="center" src="https://github.com/SFGLab/nf-hichip/blob/main/nf_HiChIP_pipeline.png">
+</p>
 
-The pipeline is presented on the following figure:
+-------
+## Introduction
 
-![Figure 1](hichip_nf_pipeline.png)
+We have developed an nf-HiChIP pipeline that combines the analytical approach designed for ChIP-seq data processing (mapping, filtering, peak calling, coverage tracks calculations) with HiChIP-specific analysis (MAPS pipeline, Juric, Ivan, et al.). This pipeline enables users to conduct thorough and efficient analysis of multiple HiChIP datasets simultaneously, eliminating the requirement for additional ChIP-seq experiments.
 
-To use the pipeline, you need to have nextflow installed.
+-------
+## Working with nf-HiChIP pipeline
 
-To run, use command: 
+#### Step 1.
+[Docker](https://hub.docker.com/) image available:
+```
+https://hub.docker.com/repository/docker/mateuszchilinski/hichip-nf-pipeline/general
+```
+Command to run Docker image (use -v to bind folder with data):
+```
+docker run -v /path_to_your_data/:/data_in_container/ -it mateuszchilinski/hichip-nf-pipeline:latest
+```
+#### Step 2.
+To run, use the command inside the container use: 
 
-```nextflow run main.nf --design design.csv```
-
-Example design.csv file:
+```
+nextflow run main.nf --design design.csv
+```
+#### Step 3.
+Example for design.csv file:
 
 sample | fastq_1 |fastq_2 | replicate |
 -- | ------ |------ | ------ |
@@ -22,3 +37,28 @@ S1 | /data/SAMPLE1_2_R1.fastq.gz | /data/SAMPLE1_2_R2.fastq.gz | 2
 S2 | /data/SAMPLE2_1_R1.fastq.gz | /data/SAMPLE2_1_R2.fastq.gz | 1
 S2 | /data/SAMPLE2_2_R1.fastq.gz | /data/SAMPLE2_2_R2.fastq.gz | 2
 
+#### Step 4.
+The parameters of the pipeline can be found in the following table. All of them are optional: 
+
+Parameter | Description | Default |
+-- | ------ |------ |
+--ref | Reference genome for the analysis. | /workspaces/hichip-nf-pipeline/ref/Homo_sapiens_assembly38.fasta
+--outdir | Folder with the final results. | results
+--design | .csv file containing information about samples and replicates. | /workspaces/hichip-nf-pipeline/design_high.csv
+--chrom_sizes | Sizes of chromosomes for the specific reference genome. | /workspaces/hichip-nf-pipeline/hg38.chrom.sizes
+--threads | Threads to use in each task. | 4
+--mem | Memory to use (in GB) for sorting task. | 4
+--mapq | MAPQ for MAPS. | 30
+--peak_quality | Quality parameter (q-value (minimum FDR) cutoff) for MACS3. | 0.05
+--genome_size | Genome size string for MACS3. | hs
+
+#### Step 5.
+For Post-processing and figure recreation, please follow the scripts in the folder [post_processing](https://github.com/SFGLab/nf-hichip/tree/main/post_processing)
+
+-------
+## Citation
+If you use nf-HiChIP in your research (the idea, the algorithm, the analysis scripts, or the supplemental data), please give us a star on the GitHub repo page and cite our paper as follows:    
+
+- Official version  --
+- Preprint bioRxiv --
+-------