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Researchers collaborating from different locations need a method to capture and store scientific workflow provenance that guarantees provenance integrity and reproducibility. As modern science is moving towards greater data accessibility, researchers also need a platform for open access data sharing. We propose SciLedger, a blockchain-based platform that provides secure, trustworthy storage for scientific workflow provenance to reduce research fabrication and falsification. SciLedger utilizes a novel invalidation mechanism that only invalidates necessary provenance records. SciLedger also allows for workflows with complex structures to be stored on a single blockchain so that researchers can utilize existing data in their scientific workflows by branching from and merging existing workflows. Our experimental results show that SciLedger provides an able solution for maintaining academic integrity and research flexibility within scientific workflows.