https://github.com/zsteve/nf-atac
ATAC-seq pipeline written in Nextflow
https://github.com/zsteve/nf-atac
atac-seq bioinformatics epigenomics nextflow ngs pipeline
Last synced: 9 days ago
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ATAC-seq pipeline written in Nextflow
- Host: GitHub
- URL: https://github.com/zsteve/nf-atac
- Owner: zsteve
- License: mit
- Created: 2018-01-24T23:05:25.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-10-08T05:45:11.000Z (about 7 years ago)
- Last Synced: 2025-09-07T02:02:09.894Z (about 1 month ago)
- Topics: atac-seq, bioinformatics, epigenomics, nextflow, ngs, pipeline
- Language: Nextflow
- Homepage:
- Size: 41 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
**nf-ATAC**
_An integrated pipeline for ATAC-seq data written in *Nextflow* with:heart:_
Author: Stephen Zhang (stephen.zhang@monash.edu)
Date: 5 Feb 2018
*Introduction*
`nf-ATAC` pipeline for processing ATAC-seq data written in Nextflow script (https://www.nextflow.io/).
Currently in early stages, this `README` will definitely be updated regularly (check often!)
Have an problem? Please log an issue on GitHub (https://github.com/zsteve/atac-seq-pipeline)
*Dependencies*
Please make sure these tools are installed before running the pipeline:
* [`MACS2`](https://github.com/taoliu/MACS)
* [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* [`cutadapt`](http://cutadapt.readthedocs.io/en/stable/guide.html)
* [`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
* [`picard/2.8.2`](https://broadinstitute.github.io/picard/)
* [`samtools`](http://samtools.sourceforge.net/)
* [`homer`](http://homer.ucsd.edu/homer/) please add to $PATH
* [`jvarkit`](https://github.com/lindenb/jvarkit) *only need to use samjs*
* [`snakeyaml`](https://bitbucket.org/asomov/snakeyaml/wiki/Documentation) please add to $CLASSPATH
* [`sambamba`](http://lomereiter.github.io/sambamba/) please add to $PATH
For QC, we require the following:
* [`ATACseqQC`](https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html)
* [`Biostrings`](https://bioconductor.org/packages/release/bioc/html/Biostrings.html)
* [`GenomicFeatures`](https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html)
* [`GenomeInfoDb`](https://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html)
* [`ChIPpeakAnno`](https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html)
* [`MotifDb`](http://bioconductor.org/packages/release/bioc/html/MotifDb.html)
One can check that most dependencies are installed by running `checkdep.sh`.
*At the current time, please manually confirm that `snakeyaml` is installed!
*Installing Nextflow*
Nextflow can be downloaded by using the following command:
`curl -s https://get.nextflow.io | bash`
This will create a binary `nextflow` in the working directory. You can add this binary to your `PATH` for ease of use:
`export PATH=$PATH:[your path here]`
The pipeline can be executed by running `nextflow`, specifying the script and relevant commandline arguments.
`nextflow .nf <command line arguments>`
*Running the pipeline - single sample*
_Data preparation_
Paired-end read sample data in `.fastq.gz` format should be located in a directory with the desired sample name. Read pairs should be distinguishable in the format `*_R{1,2}*.fastq.gz`.
_Configuration_
There are a few parameters which *must* be specified correctly in `config.yaml` before running the pipeline ... **things will not work without these parameters**
* `macs2 : --gsize` must be specified for `macs2` to correctly call peaks.
* `qc_report : bsgenome, txdb` must be specified for QC report generation using `ATACseqQC` to work. `bsgenome` must specifiy the BSgenome Biostrings package corresponding to the reference genome. `txdb` must specify the `GenomeFeatures` package containing transcript annotations for the reference genome.
_Command_
Nextflow will create a `work` directory (containing pipeline data) in its working directory (i.e. `.`). Final pipeline output files will be output to a desired directory, however these will generally be _symlinks_ to the actual copy of the file within `work/**/your_file_here`. It is *very* important that `work` does *not* get deleted - otherwise your symlinks will mean nothing!
```
nextflow atac_pipeline.nf --num-cpus $NUM_CPUS
--jvarkit-path $JVARKIT_PATH
--input-dir $INPUT_DIR
--output-dir $OUTPUT_DIR
--config-file $CONFIG_FILE
--ref-genome-name $GENOME_NAME
--ref-genome-index $GENOME_INDEX
--ref-genome-fasta $GENOME_FASTA
```
* `NUM_CPUS` - maximum number of CPUs to use for the _entire_ pipeline
* `INPUT_DIR` - path of the directory containing R1,R2 data
* `OUTPUT_DIR` - path of the directory to write outputs to (will be created if it doesn't already exist). This can be the same as INPUT_DIR.
* `CONFIG_FILE` (OPTIONAL) - path to `config.yaml` (in case one wants custom parameters for pipeline components).
* `GENOME_NAME` - name of the reference genome (e.g. `danRer10`, `hg18`)
* `GENOME_INDEX` - path to `bowtie2` indexes for reference genome
* `GENOME_FASTA` - path to `FASTA` sequence of reference genome
* `JVARKIT_PATH` - path to installation of `jvarkit`.
Nextflow will output its data to your directory of choice.
*Running the pipeline - multiple samples*
_Data preparation_
For each sample, create a folder `SAMPLE_ID/` containing the paired-end read data in `fastq.gz` format. Create a *sample table* as a text file:
* Each line corresponds to *one* sample. Fields are as follows:
```
[Sample_ID] [path to sample input directory] [path to sample output directory]
```
_Command_
Pipeline will read in samples from the sample table `.txt` file and attempt to process those samples in _parallel_.
```
nextflow atac_pipeline.nf --num-cpus $NUM_CPUS
--jvarkit-path $JVARKIT_PATH
--config-file $CONFIG_FILE
--multi-sample
--sample-table $SAMPLE_TABLE
--ref-genome-name $GENOME_NAME
--ref-genome-index $GENOME_INDEX
--ref-genome-fasta $GENOME_FASTA
```