Verified Commit c5d0e4fe authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
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new gitlab URL

parent c794b217
...@@ -11,5 +11,5 @@ ...@@ -11,5 +11,5 @@
- [Singularity](https://sylabs.io/singularity/) using a docker image published on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq) - [Singularity](https://sylabs.io/singularity/) using a docker image published on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq)
- [AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`) - [AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`)
- add [FastqScreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) - add [FastqScreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
- drop `DESeq2` for contrast in favor to the dedicated tool: [`DiffBind`](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) - drop `DESeq2` for contrast in favor to the dedicated tool: [`DiffBind`](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) #TODO
- don't import the IGV session in report, the HTML becomes too large - don't import the IGV session in report, the HTML becomes too large
\ No newline at end of file
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
[![Snakemake](https://img.shields.io/badge/snakemake-≥6.4.0-brightgreen.svg)](https://snakemake.github.io) [![Snakemake](https://img.shields.io/badge/snakemake-≥6.4.0-brightgreen.svg)](https://snakemake.github.io)
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. This [workflow](https://gitlab.lcsb.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 ## Overview
...@@ -77,7 +77,7 @@ and run the following commands: ...@@ -77,7 +77,7 @@ and run the following commands:
```bash ```bash
VERSION="v0.0.9" VERSION="v0.0.9"
wget -qO- https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq/-/archive/${VERSION}/snakemake-chip-seq-.tar.gz | tar xfz - --strip-components=1 wget -qO- https://gitlab.lcsb.uni.lu/aurelien.ginolhac/snakemake-chip-seq/-/archive/${VERSION}/snakemake-chip-seq-.tar.gz | tar xfz - --strip-components=1
``` ```
this command will download, extract (without the root folder) the following files: this command will download, extract (without the root folder) the following files:
......
[**ChIP-seq** peak-calling, QC and differential analysis pipeline](https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-chip-seq), **ChIP-seq** peak-calling, QC and differential analysis pipeline https://gitlab.lcsb.uni.lu/aurelien.ginolhac/snakemake-chip-seq,
derived from [Snakemake template](https://github.com/snakemake-workflows/chipseq) (itself port of the `nextflow pipeline <https://nf-co.re/chipseq>`_). derived from the Snakemake template https://github.com/snakemake-workflows/chipseq
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