HiIP run¶

1. About¶

The HiIP executable is composed of several inter-related sub commands. Please see HiIP -h for all available options.

This part of the documentation describes options and concepts for HiIP run sub command in more detail. With minimal configuration, the run sub command enables you to start running HiIP pipeline.

Setting up the HiIP pipeline is fast and easy! In its most basic form, HiIP run only has four required inputs.

2. Synopsis¶

$ HiIP run [--help] \
      [--dry-run] [--job-name JOB_NAME] [--mode {slurm,local}] \
      [--sif-cache SIF_CACHE] [--singularity-cache SINGULARITY_CACHE] \
      [--silent] [--threads THREADS] [--tmp-dir TMP_DIR] [--CTCF] \
      --input INPUT [INPUT ...] \
      --output OUTPUT \
      --genome GENOME \
      --chip-peaks ChIP_PEAKS

The synopsis for each command shows its arguments and their usage. Optional arguments are shown in square brackets.

A user must provide a list of FastQ (globbing is supported) to analyze via --input argument, an output directory to store results via --output argument, a reference genome via the --genome option, and peakcalls from a ChIP-seq experiment via the --chip-peaks option.

Use you can always use the -h option for information on a specific command.

2.1 Required arguments¶

Each of the following arguments are required. Failure to provide a required argument will result in a non-zero exit-code.

--input INPUT [INPUT ...]

Input FastQ or BAM file(s).
type: file(s)

One or more FastQ files can be provided. The pipeline does NOT support single-end data. From the command-line, each input file should seperated by a space. Globbing is supported! This makes selecting FastQ files easy. Input FastQ files should always be gzipp-ed.

Example: --input .tests/*.R?.fastq.gz

--output OUTPUT

Path to an output directory.
type: path

This location is where the pipeline will create all of its output files, also known as the pipeline's working directory. If the provided output directory does not exist, it will be created automatically.

Example: --output /data/$USER/HiIP_out

--genome GENOME

Reference genome.
type: hg38 or mm10

This option defines the reference genome of the samples. HiIP does comes bundled with prebuilt reference files from GENCODE for human and mouse samples. Please select from one of the following options: hg38 or mm10.

Example: --genome hg38

--chip-peaks ChIP_PEAKS

Peak calls from ChIP-seq experiment.
type: file

This can be ChIP-seq peak calls from your own experiment or from a public database like ENCODE. File formats accepted are BED, narrowPeak, and broadPeak. Please see this link for more information about this input file.

Example: --chip-peaks ENCFF017XLW.bed

2.2 Analysis options¶

--CTCF

Identify chromatin loops.
type: boolean flag default: False

Please provide this option if the IP was done on CTCF or a cohesin subunit. Do NOT provide this option if the IP was done on an enhancer or active promotor marker, i.e. H3K27ac or H3K4me3.

Example: --CTCF

2.3 Orchestration options¶

Each of the following arguments are optional, and do not need to be provided.

--dry-run

Dry run the pipeline.
type: boolean flag

Displays what steps in the pipeline remain or will be run. Does not execute anything!

Example: --dry-run

--silent

Silence standard output.
type: boolean flag

Reduces the amount of information directed to standard output when submitting master job to the job scheduler. Only the job id of the master job is returned.

Example: --silent

--mode {slurm,local}

Execution Method.
type: string
default: slurm

Execution Method. Defines the mode or method of execution. Vaild mode options include: slurm or local.

slurm
The slurm execution method will submit jobs to the SLURM workload manager. It is recommended running HiIP in this mode as execution will be significantly faster in a distributed environment. This is the default mode of execution.

local
Local executions will run serially on compute instance. This is useful for testing, debugging, or when a users does not have access to a high performance computing environment. If this option is not provided, it will default to a local execution mode.

Example: --mode slurm

--job-name JOB_NAME

Set the name of the pipeline's master job.
type: string default: pl:HiIP

When submitting the pipeline to a job scheduler, like SLURM, this option always you to set the name of the pipeline's master job. By default, the name of the pipeline's master job is set to "pl:HiIP".

Example: --job-name pl_id-42

--singularity-cache SINGULARITY_CACHE

Overrides the $SINGULARITY_CACHEDIR environment variable.
type: path
default: --output OUTPUT/.singularity

Singularity will cache image layers pulled from remote registries. This ultimately speeds up the process of pull an image from DockerHub if an image layer already exists in the singularity cache directory. By default, the cache is set to the value provided to the --output argument. Please note that this cache cannot be shared across users. Singularity strictly enforces you own the cache directory and will return a non-zero exit code if you do not own the cache directory! See the --sif-cache option to create a shareable resource.

Example: --singularity-cache /data/$USER/.singularity

--sif-cache SIF_CACHE

Path where a local cache of SIFs are stored.
type: path

Uses a local cache of SIFs on the filesystem. This SIF cache can be shared across users if permissions are set correctly. If a SIF does not exist in the SIF cache, the image will be pulled from Dockerhub and a warning message will be displayed. The HiIP cache subcommand can be used to create a local SIF cache. Please see HiIP cache for more information. This command is extremely useful for avoiding DockerHub pull rate limits. It also remove any potential errors that could occur due to network issues or DockerHub being temporarily unavailable. We recommend running HiIP with this option when ever possible.

Example: --singularity-cache /data/$USER/SIFs

--threads THREADS

Max number of threads for each process.
type: int
default: 2

Max number of threads for each process. This option is more applicable when running the pipeline with --mode local. It is recommended setting this vaule to the maximum number of CPUs available on the host machine.

Example: --threads 12

--tmp-dir TMP_DIR

Max number of threads for each process.
type: path
default: /lscratch/$SLURM_JOBID

Path on the file system for writing temporary output files. By default, the temporary directory is set to '/lscratch/$SLURM_JOBID' for backwards compatibility with the NIH's Biowulf cluster; however, if you are running the pipeline on another cluster, this option will need to be specified. Ideally, this path should point to a dedicated location on the filesystem for writing tmp files. On many systems, this location is set to somewhere in /scratch. If you need to inject a variable into this string that should NOT be expanded, please quote this options value in single quotes.

Example: --tmp-dir /scratch/$USER/

2.4 Miscellaneous options¶

Each of the following arguments are optional, and do not need to be provided.

-h, --help

Display Help.
type: boolean flag

Shows command's synopsis, help message, and an example command

Example: --help

3. Example¶

# Step 1.) Grab an interactive node,
# do not run on head node!
srun -N 1 -n 1 --time=1:00:00 --mem=8gb  --cpus-per-task=2 --pty bash
module purge
module load singularity snakemake

# Step 2A.) Dry-run the pipeline
./HiIP run --input .tests/*.R?.fastq.gz \
                  --output /data/$USER/output \
                  --mode slurm \
                  --CTCF \
                  --dry-run

# Step 2B.) Run the HiIP pipeline
# The slurm mode will submit jobs to 
# the cluster. It is recommended running 
# the pipeline in this mode.
./HiIP run --input .tests/*.R?.fastq.gz \
                  --output /data/$USER/output \
                  --mode slurm \
                  --CTCF