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This reverts commit d89fd65.
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_Describe the problem or feature in addition to a link to the issues._ the non summary mode of validate_bam can output multiple lines _per read_ in the input BAM, using more disk than the input file. This passing that output through gzip. This also removes the x2 factor on disk size allocation for this task. We may instead want to keep that x2 factor but only if we're in full report mode? Before submitting this PR, please make sure: - [ ] You have added a few sentences describing the PR here. - [ ] The code passes all CI tests without any errors or warnings. - [ ] You have added tests (when appropriate). - [ ] You have added an entry in any relevant CHANGELOGs (when appropriate). - [ ] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [ ] You have updated the README or other documentation to account for these changes (when appropriate). --------- Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>
Add filtering of sex chromosomes to the UMAP generation. Also generate a list of probes that have SNPs. Before submitting this PR, please make sure: - [x] You have added a few sentences describing the PR here. - [x] The code passes all CI tests without any errors or warnings. - [ ] You have added tests (when appropriate). - [x] You have added an entry in any relevant CHANGELOGs (when appropriate). - [x] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [ ] You have updated the README or other documentation to account for these changes (when appropriate). --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Ari Frantz <ari.frantz@stjude.org> Co-authored-by: Jobin Sunny <38107318+jsunny23@users.noreply.github.com>
Currently, we compute file sizes in `GiB`. We then use those to request disk space, but in `GB`. This is silently undercounting the amount of disk space we need for these tasks. `GB` was chosen to be the common unit because our variables already end in `_gb` so this is the least disruptive change. Before submitting this PR, please make sure: - [x] You have added a few sentences describing the PR here. - [ ] The code passes all CI tests without any errors or warnings. - [ ] You have added tests (when appropriate). - [x] You have added an entry in any relevant CHANGELOGs (when appropriate). - [ ] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [ ] You have updated the README or other documentation to account for these changes (when appropriate).
_Describe the problem or feature in addition to a link to the issues._ Before submitting this PR, please make sure: - [ ] You have added a few sentences describing the PR here. - [ ] The code passes all CI tests without any errors or warnings. - [ ] You have added tests (when appropriate). - [ ] You have added an entry in any relevant CHANGELOGs (when appropriate). - [ ] If you have made any changes to the `scripts/` or `docker/` directories, please ensure any image versions have been incremented accordingly! - [ ] You have updated the README or other documentation to account for these changes (when appropriate).
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![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
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Snyk Container found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.
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all tests passing 🎉 |
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I haven't gotten further, but my assumption was that we'd call sprocket dev test as the second part of this to test the newly built images.
| with: | ||
| lint: true | ||
| except: KnownRules | ||
| sprocket_lint: |
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If we're doing lint and format, I'd probably just shorten this to sprocket.
| sprocket_lint: | |
| sprocket: |
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Or maybe lengthen to sprocket_lint_format
| String stringency_arg = if index_validation_stringency_less_exhaustive | ||
| then "--INDEX_VALIDATION_STRINGENCY LESS_EXHAUSTIVE" | ||
| else "" |
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I don't recall what this parameter does. Why are we removing the argument?
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This PR is for demonstration purposes of the RFC document herethis PR has morphed from a demonstration into a real PR for swapping our test infra from pytest to Sprocket. Still a WIP as not all the tests are written yet and it has not been hooked into CI yet