updated code with changes for handling 1 row per sample per cycle and 1 row per sample samplesheets #23
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new format is sample,cycle_number,channel_count,image_tiles
…cles and channels
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I looked through the changes.
I like the flexibility of the sample sheet, it is a bit complex at first, but it then makes sense.
I think that the testing is a bit messy regarding which are the inputs and the outputs, and what is being tested. And yeah the workflow sections have to be filled out and tests run.
The tests can probably be refactored now that the workflow inputs are more logical with the new template layout. I will have a better idea about that by the end of the week when I finish that refactor/merge. |
* Remove defaults in nf-test.config and mark schema for staging * Remove extra copy of schema since we are now staging the main instance * Change nf-test local nextflow.config so it only contains overrides
* Remove more unused/duplicate nextflow config files * Update test inputs to match new pipeline inputs * Generate snapshot for versions output
Resources should be specifed via label in the module itself
…licated. will try to simplify next
…f-core into sample_sheet_mod
* Add CsvUtils helper class, currently just for rounding float columns. * Round float columns in quantification output csv content to avoid false snapshot mismatch due to precision issues in lowest bits.
…f-core into sample_sheet_mod
* Ran nf-core modules update deepcell/mesmer * Deleted local mesmer patch as it's no longer necessary * Adjusted modules config to eliminate containerOptions (not needed any longer) and manually set the prefix to match our previous locally patched behavior * Added test config to mount the local /tmp/.keras in the container at the same path to provide caching of the ~100 MB model file the container downloads at runtime * Updated test snapshot for new version number
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Amazing work @jmuhlich, |
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Sorry to pull the rug out from folks who have reviewed, but after I started making substantial updates to this branch it got rather out of date with Rob's original version and we decided it would be best to create a new PR. So I'm closing this in favor of #29. |
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).