Commit b1bb6953 authored by Xavier Grand's avatar Xavier Grand
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Beginning of Readme redaction

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# nextflow pipeline
# ChIPster
This repository is a template and a library repository to help you build nextflow pipeline.
You can fork this repository to build your own pipeline.
ChIPster is a nextflow pipeline dedicated to analyse ChIPseq data.
## Getting the last updates
To get the last commits from this repository into your fork use the following commands:
For the first time:
```sh
git remote add upstream git@gitbio.ens-lyon.fr:pipelines/nextflow.git
git pull upstream master
```
Then to make an update:
```sh
git pull upstream master
git merge upstream/master
git clone git@gitbio.ens-lyon.fr:xgrand/ChIPster.git
```
## Getting Started
These instructions will get you a copy of the project as a template when you want to build your own pipeline.
[you can follow them here.](doc/getting_started.md)
## Building your pipeline
You can follow the [building your pipeline guide](./doc/building_your_pipeline.md) for a gentle introduction to `nextflow` and taking advantage of this template to build your pipelines.
## Existing Nextflow pipeline
Before starting a new project, you can check if someone else didn’t already to the work !
- [on the nextflow project page](./doc/nf_projects.md)
- [on the nf-core project](https://nf-co.re/pipelines)
The pipeline `src/chipster.nf` works with a configuration file in **Yaml** containing experiment information and a nextflow configuration file `src/nextflow.config`.
The arguments of this pipeline are described in the table below:
| Arguments | Description |
|:---------------------------:|:-------------------------------------------------------------------:|
| -c | configuration file. This parameter should always be `src/nextflow.config` |
| -profile | The profile to use. This can be **docker** or **singularity** to run the pipeline in docker or singularity container respectively. This can also be **psmn** to launch the analysis on the PSMN |
| -params-file | A **yaml** configuration file containing experiement information required for analysis |
The composition of **Yaml** parameters file is described in the following table:
| Arguments | Description |
|:---------------------------:|:-------------------------------------------------------------------:|
| paired_end | Boolean to setup sequencing type (paired-end or single-end), default = false |
| fastq_folder | Directory containing fastq files (rawdata) |
| genome | Path to the reference genome fasta file |
| genome_size | Entire genome size (hg19 = 2913022398) |
| chrom_sizes | A file containing chromosome sizes (usualy "chrom.sizes" file) |
| idx | Directory containing previously indexed genome files with bowtie2 or "" (empty string to perform the indexation during the pipeline analysis) |
| project | Project name to prefix results directories and files |
| input | Balise of input data |
| row<n> | Corresponds to the balise of the n sample |
| sample | Sample must be a string. It corresponds to the name of the sample |
| fastq | The corresponding fastq file, can be compressed as gz file |
| condition | Condition name, must be the same for IP and Input corresponding samples |
| type | "IP" or "Input" corresponding to sample type |
## Contributing
......@@ -41,9 +46,8 @@ If you want to add more tools to this project, please read the [CONTRIBUTING.md]
## Authors
* **Laurent Modolo** - *Initial work*
See also the list of [contributors](https://gitbio.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
* **Xavier Grand** - *Maintainer*
* **Laurent Modolo** - *template work*
## License
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