This workflow is a Snakemake port of the [nextflow chipseq pipeline](https://nf-co.re/chipseq) and performs ChIP-seq peak-calling, QC and differential analysis.
This [workflow](https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq) is derived from [Snakemake template](https://github.com/snakemake-workflows/chipseq)(itself port of the [nextflow chipseq pipeline](https://nf-co.re/chipseq)) and performs ChIP-seq peak-calling, QC and differential analysis.
## Overview
As displayed in the final [**report**](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/report.html) the pipeline looks like:

## Install
On the [UL-HPC](https://hpc.uni.lu/), what is needed is:
-`snakemake`, version at least `6.4`
-`singularity`, provided the HPC as an **EasyBuild module**.
- this workflow template
For snakemake, you could install it via conda
and installing snakemake as in the RFTM
### Install conda
- Follow the instructions from **Sarah Peter** in her [tutorial](https://r3.pages.uni.lu/school/snakemake-tutorial/#conda for installing `Miniconda3` (downloading 90 MB).
Once `(base)`*conda* activated, you can update your `snakemake` version with:
`mamba upgrade -n snakemake snakemake`
## Usage
The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/chipseq).
After booking ressources on the access node, like for example here, 1 hour and 6 cores:
this is the easy part as the [HPC team](https://hpc.uni.lu/about/team.html) is providing us with available [modules](https://hpc.uni.lu/users/software/)
the command once on a `node` is:
```bash
(base) user@access module load tools/Singularity
```
### Conda activate
```bash
(base) user@access $ conda activate snakemake
```
Of note, the 2 above steps can be replaced by the alias `smk` if you added the alias in your `.bashrc`
This template is derived from the official [Snakemake-workflow](https://github.com/snakemake-workflows/chipseq) by [Antonie Vietor](https://github.com/AntonieV) and [David Laehnemann](https://github.com/dlaehnemann).
Initially a port of the [Next-Flow ChIP-seq](https://nf-co.re/chipseq)(https://doi.org/10.5281/zenodo.3240506) by [Harshil Patel](https://github.com/drpatelh)[et al.](https://github.com/nf-core/chipseq/graphs/contributors)
## Main changes
-[Singularity](https://sylabs.io/singularity/) using a docker image publish on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq)
-[AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`)