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View Code? Open in Web Editor NEWStandardized workflows for AMP-AD data processing and analysis
Standardized workflows for AMP-AD data processing and analysis
Originally, this repo was intended to host multiple workflows for amp-ad data processing. We have decided that this was not the best idea and we should host shareable tools and workflows separately. The RNASeq workflow (https://github.com/Sage-Bionetworks/amp-workflows/tree/develop/amp-rnaseq_reprocessing/amp-rnaseq_reprocess-workflow) should be migrated to https://github.com/Sage-Bionetworks/RNASeq-CWL-Workflow
Rather than using symlinks to tools in this repo, any shareable CWL tools and dockerfiles should be migrated to https://github.com/Sage-Bionetworks/RNASeq-CWLTools.
Currently, this repo contains a mixture of inline Python CWL tools (https://github.com/Sage-Bionetworks/amp-workflows/blob/develop/tools/python_utils/upload_synapse.cwl, for example) and tools that use docker images containing python scripts (https://github.com/Sage-Bionetworks/amp-workflows/tree/develop/docker/python_utils). This should be standardized such that we consistently use a single strategy for handling python code
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