weave run

Objective¶

weave's run subcommand is the command line entrypoint for execution of the Illumnia demultiplexing and FASTQ QC/QA pipeline.

Given a run id or run directory containing the artifacts produced by Illumnia MiSeq/NextSeq/HiSeq instruments (RTAComplete.txt) this workflow will demultiplex all the reads and run an array of tools for evaluating the qualitying of the sequenced reads.

The ultimate output for this workflow is a MultiQC report containing all the subsequent metrics from the QC/QA portions of the pipeline.

The penultimate output for this workflow is a cohort of fastq.gz files deconvoluted from their adapter information and seperated into

Method signature¶

weave run [-h] 
    [-s/--seq_dir <sequencing directory>] 
    [-o/--output <output directory>] 
    [-d/--dry-run] 
    [-n/--noqc] 
    [-l/--local] 
    <run directory> [<run directory> ...]

Example¶

Setup¶

# Step 1.) Grab an interactive node,
# do not run on head node!
sinteractive

# Step 2.) Follow install directions
source ~/.my_virtual_environment/bin/activate

Dependencies¶

Ensure that snakemake and singularity are loaded and $PATH accessible.

If executing from biowulf cluster:

# Step 3.) module load snakemake and depdenencies 
module purge
module load singularity snakemake

If executing from BigSky cluster:

# Step 4.) spack load snakemake and depdenencies
source /gs1/RTS/OpenOmics/bin/dependencies.sh

Execution¶

# Step 4A.) Dry-run the weave pipeline
./weave run <run id> \
                  --output /data/$USER/output \
                  --dry-run

# Step 4B.) Run the weave pipeline
# The slurm mode will submit jobs to 
# the cluster. It is recommended running 
# the pipeline in this mode.
./weave run <run id> \
                  --output /data/$USER/output \

Run Identifiers (runid)¶

Run identifiers are strings that uniquely identify a particular sequencing run and are of the format:

DATE<YYMMDD>_INSTRUMENTID_TIME<24hr>_FLOWCELLID

Arguments¶

Required¶

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

<run directory> [<run directory> ...]

Input runid or run directory.
type: strings(s)/path(s)

One or more IDs or directories can be provided and the pipeline will run them. It is not necessary to specify server configuration information such as data parent directory, unless you on a non-standard cluster.

Example: 220729_NB551182_0219_AHGGJNBGXK

--output OUTPUT

Path to the top-level output directory.
type: strings(s)/path(s)

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

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

Optional¶

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

--local

Execute locally instead of through a cluster executor
type: boolean flag

This flag will trigger the workflow to run in the local terminal as a blocking process.

Example: --local