Tags and Filtering

Tags let you organize rules into logical groups and selectively run subsets of your workflow.

Assigning Tags

Add tags to any rule in your Oxymakefile.toml:

[rule.align]
input = ["data/{sample}.fastq"]
output = ["aligned/{sample}.bam"]
shell = "bwa mem ref.fa {input} | samtools sort > {output}"
tags = ["alignment", "compute-heavy"]

[rule.qc]
input = ["aligned/{sample}.bam"]
output = ["qc/{sample}_report.html"]
shell = "fastqc {input} -o qc/"
tags = ["qc", "fast"]

Filtering by Tag

Run only jobs matching a tag:

ox run --tag alignment        # Only alignment jobs
ox run --tag qc               # Only QC jobs
ox run --tag compute-heavy    # Only compute-heavy jobs

Exclude jobs by tag:

ox run --exclude-tag slow     # Skip slow jobs

Tag-Based DAG Views

Tags integrate with the DAG visualization:

ox dag --group-by tag         # Group nodes by tag in the DAG view
ox plan --tag alignment       # Show plan for alignment jobs only

Hierarchical Organization

Use dotted tag names for hierarchy:

tags = ["pipeline.alignment", "resource.gpu"]

This enables filtering at different levels:

ox run --tag "pipeline.*"         # All pipeline stages
ox run --tag "resource.gpu"       # Only GPU jobs

Use Cases

• Selective re-runs: Re-run only QC after parameter changes
• Resource-based scheduling: Tag GPU vs CPU jobs for different executors
• Stage grouping: Organize large workflows into logical phases
• Development iteration: Run only the stage you are working on

Next Steps

• The Three Graphs -- how tags affect DAG visualization
• Execution Modes -- how jobs are executed