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Add Snakemake workflow for QA pipelines#2

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mvdoc wants to merge 2 commits into
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claude/setup-snakemake-pipelines-SiCGC
Draft

Add Snakemake workflow for QA pipelines#2
mvdoc wants to merge 2 commits into
masterfrom
claude/setup-snakemake-pipelines-SiCGC

Fix issues in Snakemake workflow

6b0b120
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