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_Describe the problem or feature in addition to a link to the issues._ closes #277 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>
Adding an initial set of instructions for Copilot specific to WDL and our internal best practices. 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). - [ ] 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).
…60113 (#288)  ### Snyk has created this PR to fix 2 vulnerabilities in the dockerfile dependencies of this project. Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image. #### Snyk changed the following file(s): - `docker/util/Dockerfile` We recommend upgrading to `ubuntu:24.04`, as this image has only **8** known vulnerabilities. To do this, merge this pull request, then verify your application still works as expected. #### Vulnerabilities that will be fixed with an upgrade: | | Issue | Score | :-------------------------:|:-------------------------|:-------------------------  | Out-of-bounds Write <br/>[SNYK-UBUNTU2404-GNUPG2-14849555](https://snyk.io/vuln/SNYK-UBUNTU2404-GNUPG2-14849555) | **281**  | Directory Traversal <br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905) | **231**  | Directory Traversal <br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905) | **231**  | Directory Traversal <br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905) | **231**  | Directory Traversal <br/>[SNYK-UBUNTU2404-PAM-11936905](https://snyk.io/vuln/SNYK-UBUNTU2404-PAM-11936905) | **231** --- > [!IMPORTANT] > > - Check the changes in this PR to ensure they won't cause issues with your project. > - Max score is 1000. Note that the real score may have changed since the PR was raised. > - This PR was automatically created by Snyk using the credentials of a real user. --- **Note:** _You are seeing this because you or someone else with access to this repository has authorized Snyk to open fix PRs._ For more information: <img src="https://api.segment.io/v1/pixel/track?data=eyJ3cml0ZUtleSI6InJyWmxZcEdHY2RyTHZsb0lYd0dUcVg4WkFRTnNCOUEwIiwiYW5vbnltb3VzSWQiOiI1YWE0Mzc4Yi1kNzA2LTRmYWEtYTAzNC04NThhYTYwNDhhOWIiLCJldmVudCI6IlBSIHZpZXdlZCIsInByb3BlcnRpZXMiOnsicHJJZCI6IjVhYTQzNzhiLWQ3MDYtNGZhYS1hMDM0LTg1OGFhNjA0OGE5YiJ9fQ==" width="0" height="0"/> 🧐 [View latest project report](https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source=github&utm_medium=referral&page=fix-pr) 📜 [Customise PR templates](https://docs.snyk.io/scan-using-snyk/pull-requests/snyk-fix-pull-or-merge-requests/customize-pr-templates?utm_source=github&utm_content=fix-pr-template) 🛠 [Adjust project settings](https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source=github&utm_medium=referral&page=fix-pr/settings) 📚 [Read about Snyk's upgrade logic](https://docs.snyk.io/scan-with-snyk/snyk-open-source/manage-vulnerabilities/upgrade-package-versions-to-fix-vulnerabilities?utm_source=github&utm_content=fix-pr-template) --- **Learn how to fix vulnerabilities with free interactive lessons:** 🦉 [Out-of-bounds Write](https://learn.snyk.io/lesson/out-of-bounds-write/?loc=fix-pr) 🦉 [Directory Traversal](https://learn.snyk.io/lesson/directory-traversal/?loc=fix-pr) [//]: # 'snyk:metadata:{"breakingChangeRiskLevel":null,"FF_showPullRequestBreakingChanges":false,"FF_showPullRequestBreakingChangesWebSearch":false,"customTemplate":{"variablesUsed":[],"fieldsUsed":[]},"dependencies":[{"name":"ubuntu","from":"noble-20250925","to":"24.04"}],"env":"prod","issuesToFix":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905"],"prId":"5aa4378b-d706-4faa-a034-858aa6048a9b","prPublicId":"5aa4378b-d706-4faa-a034-858aa6048a9b","packageManager":"dockerfile","priorityScoreList":[281,231],"projectPublicId":"c80293d7-c0f4-4d94-b297-efe1fc5caf56","projectUrl":"https://app.snyk.io/org/compbio/project/c80293d7-c0f4-4d94-b297-efe1fc5caf56?utm_source=github&utm_medium=referral&page=fix-pr","prType":"fix","templateFieldSources":{"branchName":"default","commitMessage":"default","description":"default","title":"default"},"templateVariants":["updated-fix-title","priorityScore"],"type":"auto","upgrade":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905","SNYK-UBUNTU2404-PAM-11936905"],"vulns":["SNYK-UBUNTU2404-GNUPG2-14849555","SNYK-UBUNTU2404-PAM-11936905"],"patch":[],"isBreakingChange":false,"remediationStrategy":"vuln"}' --------- Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com> Co-authored-by: adthrasher <1165729+adthrasher@users.noreply.github.com> Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.5.0 to 2.6.3. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/urllib3/urllib3/releases">urllib3's releases</a>.</em></p> <blockquote> <h2>2.6.3</h2> <h2>🚀 urllib3 is fundraising for HTTP/2 support</h2> <p><a href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3 is raising ~$40,000 USD</a> to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects <a href="https://opencollective.com/urllib3">please consider contributing financially</a> to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.</p> <p>Thank you for your support.</p> <h2>Changes</h2> <ul> <li>Fixed a security issue where decompression-bomb safeguards of the streaming API were bypassed when HTTP redirects were followed. (CVE-2026-21441 reported by <a href="https://github.com/D47A"><code>@D47A</code></a>, 8.9 High, GHSA-38jv-5279-wg99)</li> <li>Started treating <code>Retry-After</code> times greater than 6 hours as 6 hours by default. (<a href="https://redirect.github.com/urllib3/urllib3/issues/3743">urllib3/urllib3#3743</a>)</li> <li>Fixed <code>urllib3.connection.VerifiedHTTPSConnection</code> on Emscripten. (<a href="https://redirect.github.com/urllib3/urllib3/issues/3752">urllib3/urllib3#3752</a>)</li> </ul> <h2>2.6.2</h2> <h2>🚀 urllib3 is fundraising for HTTP/2 support</h2> <p><a href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3 is raising ~$40,000 USD</a> to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects <a href="https://opencollective.com/urllib3">please consider contributing financially</a> to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.</p> <p>Thank you for your support.</p> <h2>Changes</h2> <ul> <li>Fixed <code>HTTPResponse.read_chunked()</code> to properly handle leftover data in the decoder's buffer when reading compressed chunked responses. (<a href="https://redirect.github.com/urllib3/urllib3/issues/3734">urllib3/urllib3#3734</a>)</li> </ul> <h2>2.6.1</h2> <h2>🚀 urllib3 is fundraising for HTTP/2 support</h2> <p><a href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3 is raising ~$40,000 USD</a> to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects <a href="https://opencollective.com/urllib3">please consider contributing financially</a> to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.</p> <p>Thank you for your support.</p> <h2>Changes</h2> <ul> <li>Restore previously removed <code>HTTPResponse.getheaders()</code> and <code>HTTPResponse.getheader()</code> methods. (<a href="https://redirect.github.com/urllib3/urllib3/issues/3731">#3731</a>)</li> </ul> <h2>2.6.0</h2> <h2>🚀 urllib3 is fundraising for HTTP/2 support</h2> <p><a href="https://sethmlarson.dev/urllib3-is-fundraising-for-http2-support">urllib3 is raising ~$40,000 USD</a> to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects <a href="https://opencollective.com/urllib3">please consider contributing financially</a> to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.</p> <p>Thank you for your support.</p> <h2>Security</h2> <ul> <li>Fixed a security issue where streaming API could improperly handle highly compressed HTTP content ("decompression bombs") leading to excessive resource consumption even when a small amount of data was requested. Reading small chunks of compressed data is safer and much more efficient now. (CVE-2025-66471 reported by <a href="https://github.com/Cycloctane"><code>@Cycloctane</code></a>, 8.9 High, GHSA-2xpw-w6gg-jr37)</li> <li>Fixed a security issue where an attacker could compose an HTTP response with virtually unlimited links in the <code>Content-Encoding</code> header, potentially leading to a denial of service (DoS) attack by exhausting system resources during decoding. The number of allowed chained encodings is now limited to 5. (CVE-2025-66418 reported by <a href="https://github.com/illia-v"><code>@illia-v</code></a>, 8.9 High, GHSA-gm62-xv2j-4w53)</li> </ul> <blockquote> <p>[!IMPORTANT]</p> <ul> <li>If urllib3 is not installed with the optional <code>urllib3[brotli]</code> extra, but your environment contains a Brotli/brotlicffi/brotlipy package anyway, make sure to upgrade it to at least Brotli 1.2.0 or brotlicffi 1.2.0.0 to benefit from the security fixes and avoid warnings. Prefer using <code>urllib3[brotli]</code> to install a compatible Brotli package automatically.</li> </ul> </blockquote> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/urllib3/urllib3/blob/main/CHANGES.rst">urllib3's changelog</a>.</em></p> <blockquote> <h1>2.6.3 (2026-01-07)</h1> <ul> <li>Fixed a high-severity security issue where decompression-bomb safeguards of the streaming API were bypassed when HTTP redirects were followed. (<code>GHSA-38jv-5279-wg99 <https://github.com/urllib3/urllib3/security/advisories/GHSA-38jv-5279-wg99></code>__)</li> <li>Started treating <code>Retry-After</code> times greater than 6 hours as 6 hours by default. (<code>[#3743](urllib3/urllib3#3743) <https://github.com/urllib3/urllib3/issues/3743></code>__)</li> <li>Fixed <code>urllib3.connection.VerifiedHTTPSConnection</code> on Emscripten. (<code>[#3752](urllib3/urllib3#3752) <https://github.com/urllib3/urllib3/issues/3752></code>__)</li> </ul> <h1>2.6.2 (2025-12-11)</h1> <ul> <li>Fixed <code>HTTPResponse.read_chunked()</code> to properly handle leftover data in the decoder's buffer when reading compressed chunked responses. (<code>[#3734](urllib3/urllib3#3734) <https://github.com/urllib3/urllib3/issues/3734></code>__)</li> </ul> <h1>2.6.1 (2025-12-08)</h1> <ul> <li>Restore previously removed <code>HTTPResponse.getheaders()</code> and <code>HTTPResponse.getheader()</code> methods. (<code>[#3731](urllib3/urllib3#3731) <https://github.com/urllib3/urllib3/issues/3731></code>__)</li> </ul> <h1>2.6.0 (2025-12-05)</h1> <h2>Security</h2> <ul> <li>Fixed a security issue where streaming API could improperly handle highly compressed HTTP content ("decompression bombs") leading to excessive resource consumption even when a small amount of data was requested. Reading small chunks of compressed data is safer and much more efficient now. (<code>GHSA-2xpw-w6gg-jr37 <https://github.com/urllib3/urllib3/security/advisories/GHSA-2xpw-w6gg-jr37></code>__)</li> <li>Fixed a security issue where an attacker could compose an HTTP response with virtually unlimited links in the <code>Content-Encoding</code> header, potentially leading to a denial of service (DoS) attack by exhausting system resources during decoding. The number of allowed chained encodings is now limited to 5. (<code>GHSA-gm62-xv2j-4w53 <https://github.com/urllib3/urllib3/security/advisories/GHSA-gm62-xv2j-4w53></code>__)</li> </ul> <p>.. caution::</p> <ul> <li>If urllib3 is not installed with the optional <code>urllib3[brotli]</code> extra, but your environment contains a Brotli/brotlicffi/brotlipy package anyway, make sure to upgrade it to at least Brotli 1.2.0 or brotlicffi 1.2.0.0 to benefit from the security fixes and avoid warnings. Prefer using</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/urllib3/urllib3/commit/0248277dd7ac0239204889ca991353ad3e3a1ddc"><code>0248277</code></a> Release 2.6.3</li> <li><a href="https://github.com/urllib3/urllib3/commit/8864ac407bba8607950025e0979c4c69bc7abc7b"><code>8864ac4</code></a> Merge commit from fork</li> <li><a href="https://github.com/urllib3/urllib3/commit/70cecb27ca99d56aaaeb63ac27ee270ef2b24c5c"><code>70cecb2</code></a> Fix Scorecard issues related to vulnerable dev dependencies (<a href="https://redirect.github.com/urllib3/urllib3/issues/3755">#3755</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/41f249abe1ef3e20768588969c4035aba060a359"><code>41f249a</code></a> Move "v2.0 Migration Guide" to the end of the table of contents (<a href="https://redirect.github.com/urllib3/urllib3/issues/3747">#3747</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/fd4dffd2fc544166b76151a2fa3d7b7c0eab540c"><code>fd4dffd</code></a> Patch <code>VerifiedHTTPSConnection</code> for Emscripten (<a href="https://redirect.github.com/urllib3/urllib3/issues/3752">#3752</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/13f0bfd55e4468fe1ea9c6f809d3a87b0f93ebab"><code>13f0bfd</code></a> Handle massive values in Retry-After when calculating time to sleep for (<a href="https://redirect.github.com/urllib3/urllib3/issues/3743">#3743</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/8c480bf87bcefd321b3a1ae47f04e908b6b2ed7b"><code>8c480bf</code></a> Bump actions/upload-artifact from 5.0.0 to 6.0.0 (<a href="https://redirect.github.com/urllib3/urllib3/issues/3748">#3748</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/4b40616e959c0a2c466e8075f2a785a9f99bb0c1"><code>4b40616</code></a> Bump actions/cache from 4.3.0 to 5.0.1 (<a href="https://redirect.github.com/urllib3/urllib3/issues/3750">#3750</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/82b8479663d037d220c883f1584dd01a43bb273b"><code>82b8479</code></a> Bump actions/download-artifact from 6.0.0 to 7.0.0 (<a href="https://redirect.github.com/urllib3/urllib3/issues/3749">#3749</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/34284cb01700bb7d4fdd472f909e22393e9174e2"><code>34284cb</code></a> Mention experimental features in the security policy (<a href="https://redirect.github.com/urllib3/urllib3/issues/3746">#3746</a>)</li> <li>Additional commits viewable in <a href="https://github.com/urllib3/urllib3/compare/2.5.0...2.6.3">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/stjudecloud/workflows/network/alerts). </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
_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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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