Reuse another workflow

Estimated time: 9 minutes

Overview

Questions

• What is needed to re-use another Snakemake workflow?

Objectives

• Re-use parts of the BGNN_Core_Workflow Snakemake Workflow

Reusing Another Workflow

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To re-use a workflow you generally need:

• Where to find workflow? - github “hdr-bgnn/BGNN_Core_Workflow”
• What is the relative path to the Snakefile? “workflow/Snakefile”
• What tag or version to use? “1.0.0”
• What file naming convention is the workflow using?
• What dependencies must be manually installed?

See source code for the workflow https://github.com/hdr-bgnn/BGNN_Core_Workflow/blob/main/workflow/Snakefile#L19

If there is a filename mismatch you can either change your workflow or override settings in the rule.

module bgnn_core:
    snakefile:
        github("hdr-bgnn/BGNN_Core_Workflow", path="workflow/Snakefile", tag="1.0.0")

use rule generate_metadata from bgnn_core

BASH

snakemake -c1 --use-singularity DrexelMetadata/bj373514.json

Bring in additional rules from BGNN_Core_Workflow

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use rule transform_metadata from bgnn_core
use rule crop_image from bgnn_core
use rule segment_image from bgnn_core

BASH

snakemake -c1 --use-singularity Segmented/hd529k3h_segmented.png