genome-seek run¶

1. About¶

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

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

Setting up the genome-seek pipeline is fast and easy! In its most basic form, genome-seek run only has two required inputs.

2. Synopsis¶

$ genome-seek run [--help] \
      [--mode {slurm,local}] [--job-name JOB_NAME] [--batch-id BATCH_ID] \
      [--call-cnv] [--call-sv] [--call-hla] [--call-somatic] [--open-cravat] \
      [--skip-qc] [--oc-annotators OC_ANNOTATORS] [--oc-modules OC_MODULES] \
      [--pairs PAIRS] [--pon PANEL_OF_NORMALS] [--wes-mode] [--wes-bed WES_BED] \
      [--tmp-dir TMP_DIR] [--silent] [--sif-cache SIF_CACHE] \
      [--singularity-cache SINGULARITY_CACHE] \
      [--dry-run] [--threads THREADS] \
      --input INPUT [INPUT ...] \
      --output OUTPUT

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 and an output directory to store results via --output argument.

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/genome-seek_out

2.2 Analysis options¶

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

--call-cnv

Call copy number variation (CNV).
type: boolean flag

Runs additional steps to predict copy number variation.

Example: --call-cnv

--call-sv

Call structural variation (SV).
type: boolean flag

Runs additional steps to predict structural variation.

Example: --call-sv

--call-hla

Call HLA types.
type: boolean flag

Runs additional steps to call HLA types.

Example: --call-hla

--open-cravat

Run OpenCRAVAT to annotate variants.
type: boolean flag

Runs additional steps to annotate variants with OpenCRAVAT. See the Annotation Options section below for more information about what modules are included by default and how to include more modules.

Example: --open-cravat

--skip-qc

Skips over quality control steps.
type: boolean flag

When this option is provided the pipeline will not run any of its QC related steps. This means that only data processing steps will run like trimming, alignment, and variant calling. It is worth noting that we do not recommend skipping over QC; however, in certain scenarios it may make sense. This option is useful for testing changes to data processing steps or when evaluating the overall accuracy and precision of the pipeline.

Example: --skip-qc

--wes-mode

Runs the whole exome pipeline.
type: boolean flag

By default, the whole genome sequencing (WGS) pipeline is run. This option allows a user to process and analyze whole exome sequencing data. Please note when this mode is enabled, a sub-set of the WGS rules will run. Please see the option below for more information about providing a custom exome targets/capture-kit BED file.

Example: --wes-mode

--wes-bed WES_BED

Path to exome targets/capture-kit BED file.
type: BED file

This file can be obtained from the manufacturer of the target capture kit that was used. By default, a set of BED files generated from GENCODE's exon annotation for protein coding gene's exon is used. Please note: This BED file should contain at least 6 columns.

Example: --wes-bed Agilent_SS_AllExons_V7_Regions.bed

--batch-id BATCH_ID

Unique identifer for a batch of samples.
type: string default: MD5 of the sorted file of input file names

A batch identifer should be a string containing no spaces. If a batch identifer is not provided, one will be generated by taking the MD5 checksum of the sorted list of input file names. The batch identifer is added to some output file names to ensure files are not over-written when the pipeline is run with a different set of samples. This allows the pipeline to be run with extra samples without overriding some of results of a previous run.

Example: --batch-id WGS_2022-04-19

2.3 Anotation options¶

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

2.3.1 OpenCRAVAT¶

--oc-annotators OC_ANNOTATORS

List of OpenCRAVAT annotators to use.
type: string default: config/oc_annotators.cfg

Please note that one or more annotators can be provided. Multiple annotators should be seperate with a space. By default, the pipeline will annotate variants using modules in the resource bundle; however, a custom module installation path can be defined using the --oc-modules option. Annotators listed in config/oc_annotators.cfg can be skipped over my commenting them out.

Example: --oc-annotators dann dann_coding

--oc-modules OC_MODULES

Sets the path to OpenCRAVAT's modules directory.
type: path

This option overrides the default path any installed modules for OpenCRAVAT. Use this option if you have your own custom installation of OpenCRAVAT modules. An additional annotators installed the provided path can be add to config/oc_annotators.cfg. To find where OpenCRAVAT has installed its modules, please run oc config system. Also, please take caution to ensure the annotators used at run time via the --oc-annotators option exist in the provided path.

Example: --oc-modules /data/$USER/CRAVAT/modules

2.4 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 genome-seek 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:genome-seek

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:genome-seek".

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 genome-seek cache subcommand can be used to create a local SIF cache. Please see genome-seek 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 genome-seek 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/

2.5 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
./genome-seek run --input .tests/*.R?.fastq.gz \
                  --output /data/$USER/output \
                  --call-cnv --call-sv \
                  --call-hla --open-cravat \
                  --mode slurm \
                  --dry-run

# Step 2B.) Run the genome-seek pipeline
# The slurm mode will submit jobs to 
# the cluster. It is recommended running 
# the pipeline in this mode.
./genome-seek run --input .tests/*.R?.fastq.gz \
                  --output /data/$USER/output \
                  --call-cnv --call-sv \
                  --call-hla --open-cravat \
                  --mode slurm