metavirs run¶

1. About¶

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

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

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

2. Synopsis¶

$ metavirs run [--help] [--aggregate] \
     [--mode <slurm,local>] [--job-name JOB_NAME] \
     [--dry-run] [--silent] [--sif-cache SIF_CACHE] \
     [--singularity-cache SINGULARITY_CACHE] \
     [--tmp-dir TMP_DIR] [--threads THREADS] \
     [--resource-bundle RESOURCE_BUNDLE] \
      --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 file(s).
type: file(s)

One or more FastQ files can be provided. The pipeline supports single-end and paired-end data. Single-end and paired-end FastQ files can be provided to this option simultaneously. Under the hood, the pipeline will run the correct set of rules and options for a given sample. When providing each input file, please seperate each file with a space. Globbing is supported! This makes selecting FastQ files easy. Note: Input FastQ files must 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/metavirs_out

2.2 Analysis options¶

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

--aggregate

Aggregate results into one report.
type: boolean flag

Aggregates contig annotation results into one mutli-sample, project-level interactive Krona report. By default, any resulting reports will be created at a per-sample level.

Example: --aggregate

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 metavirs 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:metavirs

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:metavirs".

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 metavirs cache subcommand can be used to create a local SIF cache. Please see metavirs 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 metavirs with this option when ever possible.

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

--resource-bundle RESOURCE_BUNDLE

Path to a resource bundle downloaded with the install sub command.
type: path

The resource bundle contains the set of required reference files for processing any data. The path provided to this option will be the path to the metavirs directory that was created when running the install sub command. Please see the install sub command for more information about downloading the pipeline's resource bundle.

Example: --resource-bundle /data/$USER/refs/metavirs

--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: /tmp/

Path on the file system for writing temporary output files. By default, the temporary directory is set to '/tmp/' for increased compatibility; however, if you are running the pipeline on a target system with a dedicated scratch space, 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. Examples¶

3.1 Biowulf¶

# Step 0.) Grab an interactive node,
# do not run on head node if you are
# on a cluster, like Biowulf/BigSky!
srun -N 1 -n 1 --time=1:00:00 --mem=8gb --cpus-per-task=2 --pty bash
# Add any missing dependencies to $PATH
module purge
module load singularity
module load snakemake

# Step 1A.) Dry-run the pipeline,
# this will display what steps will 
# be run or what steps still remain.
./metavirs run --input .tests/*.gz \
    --output /data/$USER/metavirs_out \
    --mode slurm \
    --aggregate \
    --dry-run

# Step 1B.) Run the viral metagenomics
# pipeline. The slurm mode will submit 
# jobs to the cluster. We recommended 
# running metavirs in this mode, if
# you have access to a cluster like
# Biowulf or BigSky.
./metavirs run --input .tests/*.gz \
    --output /data/$USER/metavirs_out \
    --mode slurm \
    --aggregate

3.2 BigSky¶

# Step 0.) Grab an interactive node,
# do not run on head node if you are
# on a cluster, like Biowulf/BigSky!
srun -N 1 -n 1 --time=1:00:00 --mem=8gb --cpus-per-task=2 --pty bash

# Add any missing dependencies to $PATH,
# adds singularity, snakemake, and metavirs
source /gs1/RTS/OpenOmics/bin/dependencies.sh


# Step 1A.) Dry-run the pipeline,
# this will display what steps will 
# be run or what steps still remain.
metavirs run --input .tests/*.gz \
    --output /gs1/Scratch/$USER/metavirs_out \
    --mode slurm \
    --sif-cache /gs1/RTS/OpenOmics/SIFs/ \
    --resource-bundle /gs1/RTS/OpenOmics/references/metavirs/ \
    --aggregate \
    --dry-run

# Step 1B.) Run the viral metagenomics
# pipeline. The slurm mode will submit 
# jobs to the cluster. We recommended 
# running metavirs in this mode, if
# you have access to a cluster like
# Biowulf or BigSky.
metavirs run --input .tests/*.gz \
    --output /gs1/Scratch/$USER/metavirs_out \
    --mode slurm \
    --sif-cache /gs1/RTS/OpenOmics/SIFs/ \
    --resource-bundle /gs1/RTS/OpenOmics/references/metavirs/ \
    --aggregate