!!!! This pipeline is still under development !!!!
cutnrun
cutnrun is a Nextflow pipeline for CUT&RUN analysis.
Installation
git clone https://github.com/m-mahgoub/cutnrun.git
Pipeline summary
- Quality check (fastqc)
- Generate bowtie2 index for reference genome (bowtie2 )
- Mapping with bowtie2 (bowtie2 and samtools)
- Calling peaks (macs2)
- Generate bigwig files using (deeptools bamcoverage)
- Generate heatmaps (deeptools computeMatrix and plotHeatmaps)
- The command-line options for these tools can be conveniently modified in nextflow.config file
Usage
Input files:
- fastq raw reads (either paired-end or single-end), provided as a full path in the samplesheet.csv files
- Path for reference genome fasta file provided as a parameter in nextflow.config file
- Define the plotting strategy for the desired heatmaps in YAML format in “heatmap_blueprint.yaml” file (as shown in the sample file). The user can add as many plots as required, and specify:
- The name of the plot
- The paths and labels (optional) of the bed files for regions of plotting
- The paths and labels (optional) of the bigwig files to be plotted.
- These files in ii and iii can be either a sample in the current pipeline (only ID is provided), files in the local path of the environment running the Nextflow pipeline, or remote files in servers.
Requirements:
This pipeline requires the following dependencies to be installed and avaialable in the path of the environment running the pipeline:
- Nextflow >= 20.07.1. Older Nextflow versions don't support DSL2 synatax used in this pipeline and they are not comaptible.
- Singularity or Docker.
Running pipeline in local environment
with Singularity
nextflow run test.nf -profile singularity
or with Docker
nextflow run test.nf -profile docker
Running pipeline in SLURM HPC cluster
with Singularity
nextflow run test.nf -profile slurm,singularity
or with Docker
nextflow run test.nf -profile slurm,docker
Test run:
- Clone the repository
- Run the previous commands in any environment satisfying the requirements.
- Output from test run should be generated in a directory named "results". If the test run is successful, "results" directory should be identical to the directory named "testOut"
Credit:
- Sample Datasets used in this pipeline are from nf-core chipseq repository (https://github.com/nf-core/chipseq)
- Original Sample Data Sheet: https://raw.githubusercontent.com/nf-core/cutnrun-test-datasets/chipseq/design.csv