From b1bb695323ed32b8ae78e5ffdc69fdbe5170fe8e Mon Sep 17 00:00:00 2001 From: Xavier Grand <xavier.grand@ens-lyon.fr> Date: Mon, 18 Oct 2021 16:53:30 +0200 Subject: [PATCH] Beginning of Readme redaction --- README.md | 60 +++++++++++++++++++++++++++++-------------------------- 1 file changed, 32 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index df5e0ee8..2ce31911 100644 --- a/README.md +++ b/README.md @@ -1,39 +1,44 @@ -# 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 -- GitLab