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runPipeline Options
robertprior-fixstars edited this page Sep 17, 2019
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Expanded --help option essentially noting what the parameters do, which loadParamters line they effect etc.
- 1 Setup Cluster
- 2 Color Correction
- 3 Normalization
- 4 Registration
- 5 Puncta Extraction
- 6 Base Calling
- Performance Profile
- Example Batching
- Summary Reporting (link to page) / Analysis (link to page) All of above would be bullet points but thought each folder with useful scripts in the repository would have its own page with example usages and descriptions for the files under the given directory. Unsure on this as haven't used anything under these directories directly myself (i.e not through runPipeline) apart from tests/perf-profile/summarize-stat-logs.sh. Should any of these have a separate page? Note have not made pages for this yet as not sure how many should be made or if this break down makes sense.
- Troubleshooting