C I P H E R

Version 1.0.0 | Updated August 2017

Author: Carlos Guzman

E-mail: cag104@ucsd.edu

CIPHER is a data processing workflow platform for next generation sequencing data including ChIP-seq, RNA-seq, DNase-seq, MNase-seq, ATAC-seq and GRO-seq. By taking advantage of the Nextflow language, and Singularity containers, CIPHER is an extremely easy to use, and reproducible pre-processing workflow toolkit.

HELP

CIPHER has a built in help command. For more information regarding possible parameters and their meanings, open up the command line terminal and type:

nextflow run cipher.nf --help

Installation

Download or git clone this repository and install dependencies.

The only required dependencies to run CIPHER is:

• Nextflow (https://www.nextflow.io/)
• Singularity (http://singularity.lbl.gov/index.html)

CONFIG Files

Config files are tab separated text files with 5 columns for single-ended data and 6 columns for pair ended data.

Single-ended CONFIG:

sample1     sample1_rep1    /path/to/fastq.gz   control1    sample1
sample2     sample2_rep1    /path/to/fastq.gz   control1    input

Pair-ended CONFIG:

sample1     sample1_rep1    /path/to/fastq_R1.gz    /path/to/fastq_R2.gz    control1    sample1
sample2     sample2_rep1    /path/to/fastq_R1.gz    /path/to/fastq_R2.gz    control1    input

DO NOT MIX AND MATCH SINGLE AND PAIR ENDED DATA INTO THE SAME CONFIG FILE. CIPHER DOES NOT HANDLE THIS USE-CASE YET.

Where columns refer to:

• 1. MergeID - Prefix used for naming files that are merged together.
• 2. SampleID - Prefix used for naming files that are not merged together. Typically includes replicate information.
• 3. Path 1 - The file path to first FASTQ file. Typically the R1 file in pair-ended data.
• 4. Path 2 - The file path to second FASTQ file. Only required for pair-ended data. Typically the R2 file in pair-ended data.
• 5. InputID - Used to pair sample and input files for various types of sequencing data. Use - if no input file is available or needed (as is the case in RNA-seq/GRO-seq/MNase-seq/etc.
• 6. Mark - Used to differentiate sample files from input files. Use the keyword input if that sample corresponds to an input file. Otherwise use MergeID.

Running CIPHER

1) Install required dependencies

2) Create Singularity container (will require sudo access, so a container can be created on a local laptop/desktop and then transferred to the appopriate location/machine/cluster)

```
sudo singularity create -s 8000 cipher.img
```

```
sudo singularity bootstrap cipher.img Singularity
```

3) Run your workflow

```
nextflow run cipher.nf -with-singularity <cipher.img> --mode <MODE> --config <CONFIG> --fa <FASTA> --gtf <GTF> --lib <LIB> --readLen <LENGTH> [options]
```

NOTE: If not running on a cluster please set the -qs <INT> flag in order to control the number of processes that CIPHER parallelizes. Too many and the workflow will abruptly end because it runs out of memory. nextflow run -qs <INT> cipher.nf ...

NOTE: If you would like to run CIPHER without using Singularity containers, please make sure that you have installed all the required software for your specific pipeline. Tools used can be found inside the main cipher.nf script.

Example Data

Some example data to test CIPHER's workflows can be found in the example_data folder. The user should alter the config file fastq paths before running the workflow otherwise the run will fail.

Running CIPHER on a Cluster

CIPHER is possible to execute it on your computer or any cluster resource manager without modifying it.

Currently the following platforms are supported:

• Oracle/Univa/Open Grid Engine (SGE)
• Platform LSF
• SLURM
• PBS/Torque

By default the pipeline is parallelized by spanning multiple threads in the machine where the script is launched.

For example, to submit the execution to a SGE cluster edit the file named nextflow.config, in the directory where the cipher.nf file is found, with the following content:

process {
  executor='sge'
  queue='<your queue name>'
}

In doing that, tasks will be executed through the qsub SGE command, and so your pipeline will behave like any other SGE job script, with the benefit that Nextflow will automatically and transparently manage the tasks synchronisation, file(s) staging/un-staging, etc.

More information regarding the platforms Nextflow supports and how to run them can be found HERE.