added example python functions for interacting with Nextflow#18
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added example python functions for interacting with Nextflow#18
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aw-watson
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Feb 6, 2025
* Add webapp * added example python functions for interacting with Nextflow (#18) * Update nextflow in webapp and add cromwell workflows * Track nextflow job * Move report options from command to config file * Update runFaQCs outdir setting * Update output path to match the workflow name in UI * Update content container width * Update body paddings * Update content container lg width * Uncomment nextflowJobMonitor * Fix bug * Disable prop-type validation * Track pid * Test SRA workflow with cromwell * Disable workflow * Update notification toast * Update env * Update table settings * Update form title * Fix null error * Reimplement ORCiD login * Bump mongoose from 6.12.2 to 6.13.6 in /webapp/server Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.12.2 to 6.13.6. - [Release notes](https://github.com/Automattic/mongoose/releases) - [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md) - [Commits](Automattic/mongoose@6.12.2...6.13.6) --- updated-dependencies: - dependency-name: mongoose dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump path-to-regexp and express in /webapp/server Bumps [path-to-regexp](https://github.com/pillarjs/path-to-regexp) to 0.1.12 and updates ancestor dependency [express](https://github.com/expressjs/express). These dependencies need to be updated together. Updates `path-to-regexp` from 0.1.7 to 0.1.12 - [Release notes](https://github.com/pillarjs/path-to-regexp/releases) - [Changelog](https://github.com/pillarjs/path-to-regexp/blob/master/History.md) - [Commits](pillarjs/path-to-regexp@v0.1.7...v0.1.12) Updates `express` from 4.18.2 to 4.21.2 - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/4.21.2/History.md) - [Commits](expressjs/express@4.18.2...4.21.2) --- updated-dependencies: - dependency-name: path-to-regexp dependency-type: indirect - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump cross-spawn in /webapp/server Bumps and [cross-spawn](https://github.com/moxystudio/node-cross-spawn). These dependencies needed to be updated together. Updates `cross-spawn` from 6.0.5 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) Updates `cross-spawn` from 7.0.3 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) --- updated-dependencies: - dependency-name: cross-spawn dependency-type: indirect - dependency-name: cross-spawn dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump axios from 1.6.0 to 1.7.9 in /webapp/server Bumps [axios](https://github.com/axios/axios) from 1.6.0 to 1.7.9. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](axios/axios@v1.6.0...v1.7.9) --- updated-dependencies: - dependency-name: axios dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump pug from 3.0.2 to 3.0.3 in /webapp/server Bumps [pug](https://github.com/pugjs/pug) from 3.0.2 to 3.0.3. - [Release notes](https://github.com/pugjs/pug/releases) - [Commits](https://github.com/pugjs/pug/compare/pug@3.0.2...pug@3.0.3) --- updated-dependencies: - dependency-name: pug dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ejs from 3.1.9 to 3.1.10 in /webapp/server Bumps [ejs](https://github.com/mde/ejs) from 3.1.9 to 3.1.10. - [Release notes](https://github.com/mde/ejs/releases) - [Commits](mde/ejs@v3.1.9...v3.1.10) --- updated-dependencies: - dependency-name: ejs dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nodemailer and mailparser in /webapp/server Bumps [nodemailer](https://github.com/nodemailer/nodemailer) to 6.10.0 and updates ancestor dependency [mailparser](https://github.com/nodemailer/mailparser). These dependencies need to be updated together. Updates `nodemailer` from 6.9.7 to 6.10.0 - [Release notes](https://github.com/nodemailer/nodemailer/releases) - [Changelog](https://github.com/nodemailer/nodemailer/blob/master/CHANGELOG.md) - [Commits](nodemailer/nodemailer@v6.9.7...v6.10.0) Updates `mailparser` from 3.6.5 to 3.7.2 - [Release notes](https://github.com/nodemailer/mailparser/releases) - [Changelog](https://github.com/nodemailer/mailparser/blob/master/CHANGELOG.md) - [Commits](nodemailer/mailparser@v3.6.5...v3.7.2) --- updated-dependencies: - dependency-name: nodemailer dependency-type: direct:production - dependency-name: mailparser dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump braces from 3.0.2 to 3.0.3 in /webapp/server Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3. - [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md) - [Commits](micromatch/braces@3.0.2...3.0.3) --- updated-dependencies: - dependency-name: braces dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nanoid from 3.3.7 to 3.3.8 in /webapp/client Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.7 to 3.3.8. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](ai/nanoid@3.3.7...3.3.8) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump vite from 5.4.9 to 5.4.14 in /webapp/client Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.9 to 5.4.14. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.14/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.14/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ip and socks in /webapp/server Removes [ip](https://github.com/indutny/node-ip). It's no longer used after updating ancestor dependency [socks](https://github.com/JoshGlazebrook/socks). These dependencies need to be updated together. Removes `ip` Updates `socks` from 2.7.1 to 2.8.3 - [Release notes](https://github.com/JoshGlazebrook/socks/releases) - [Commits](JoshGlazebrook/socks@2.7.1...2.8.3) --- updated-dependencies: - dependency-name: ip dependency-type: indirect - dependency-name: socks dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Fix bug --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yan Xu <yxu@pn1704854.lanl.gov> Co-authored-by: yxu-lanl <38266469+yxu-lanl@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
aw-watson
added a commit
that referenced
this pull request
Feb 25, 2025
* subworkflow from readsTaxonomyAssignment * removed old RTA config * initial conversion of contigsTaxonomyAssignment to subworkflow * bind mounts moved to process directives * fixed default container behavior * connections for RTA fixed * updated Dockerfile * RTA bugfix and rework * validation aligner binds in scripts at read time * integrated contigsTaxonomyAssignment * overhauled flow of provided contig data through pipeline. added annotation * reworked contig file flow. annotation, phagefinder, antismash worked into modules * fix accidental deletion * documented more options in config * Update modules branch (#44) * Add webapp * added example python functions for interacting with Nextflow (#18) * Update nextflow in webapp and add cromwell workflows * Track nextflow job * Move report options from command to config file * Update runFaQCs outdir setting * Update output path to match the workflow name in UI * Update content container width * Update body paddings * Update content container lg width * Uncomment nextflowJobMonitor * Fix bug * Disable prop-type validation * Track pid * Test SRA workflow with cromwell * Disable workflow * Update notification toast * Update env * Update table settings * Update form title * Fix null error * Reimplement ORCiD login * Bump mongoose from 6.12.2 to 6.13.6 in /webapp/server Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.12.2 to 6.13.6. - [Release notes](https://github.com/Automattic/mongoose/releases) - [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md) - [Commits](Automattic/mongoose@6.12.2...6.13.6) --- updated-dependencies: - dependency-name: mongoose dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump path-to-regexp and express in /webapp/server Bumps [path-to-regexp](https://github.com/pillarjs/path-to-regexp) to 0.1.12 and updates ancestor dependency [express](https://github.com/expressjs/express). These dependencies need to be updated together. Updates `path-to-regexp` from 0.1.7 to 0.1.12 - [Release notes](https://github.com/pillarjs/path-to-regexp/releases) - [Changelog](https://github.com/pillarjs/path-to-regexp/blob/master/History.md) - [Commits](pillarjs/path-to-regexp@v0.1.7...v0.1.12) Updates `express` from 4.18.2 to 4.21.2 - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/4.21.2/History.md) - [Commits](expressjs/express@4.18.2...4.21.2) --- updated-dependencies: - dependency-name: path-to-regexp dependency-type: indirect - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump cross-spawn in /webapp/server Bumps and [cross-spawn](https://github.com/moxystudio/node-cross-spawn). These dependencies needed to be updated together. Updates `cross-spawn` from 6.0.5 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) Updates `cross-spawn` from 7.0.3 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) --- updated-dependencies: - dependency-name: cross-spawn dependency-type: indirect - dependency-name: cross-spawn dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump axios from 1.6.0 to 1.7.9 in /webapp/server Bumps [axios](https://github.com/axios/axios) from 1.6.0 to 1.7.9. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](axios/axios@v1.6.0...v1.7.9) --- updated-dependencies: - dependency-name: axios dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump pug from 3.0.2 to 3.0.3 in /webapp/server Bumps [pug](https://github.com/pugjs/pug) from 3.0.2 to 3.0.3. - [Release notes](https://github.com/pugjs/pug/releases) - [Commits](https://github.com/pugjs/pug/compare/pug@3.0.2...pug@3.0.3) --- updated-dependencies: - dependency-name: pug dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ejs from 3.1.9 to 3.1.10 in /webapp/server Bumps [ejs](https://github.com/mde/ejs) from 3.1.9 to 3.1.10. - [Release notes](https://github.com/mde/ejs/releases) - [Commits](mde/ejs@v3.1.9...v3.1.10) --- updated-dependencies: - dependency-name: ejs dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nodemailer and mailparser in /webapp/server Bumps [nodemailer](https://github.com/nodemailer/nodemailer) to 6.10.0 and updates ancestor dependency [mailparser](https://github.com/nodemailer/mailparser). These dependencies need to be updated together. Updates `nodemailer` from 6.9.7 to 6.10.0 - [Release notes](https://github.com/nodemailer/nodemailer/releases) - [Changelog](https://github.com/nodemailer/nodemailer/blob/master/CHANGELOG.md) - [Commits](nodemailer/nodemailer@v6.9.7...v6.10.0) Updates `mailparser` from 3.6.5 to 3.7.2 - [Release notes](https://github.com/nodemailer/mailparser/releases) - [Changelog](https://github.com/nodemailer/mailparser/blob/master/CHANGELOG.md) - [Commits](nodemailer/mailparser@v3.6.5...v3.7.2) --- updated-dependencies: - dependency-name: nodemailer dependency-type: direct:production - dependency-name: mailparser dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump braces from 3.0.2 to 3.0.3 in /webapp/server Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3. - [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md) - [Commits](micromatch/braces@3.0.2...3.0.3) --- updated-dependencies: - dependency-name: braces dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nanoid from 3.3.7 to 3.3.8 in /webapp/client Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.7 to 3.3.8. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](ai/nanoid@3.3.7...3.3.8) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump vite from 5.4.9 to 5.4.14 in /webapp/client Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.9 to 5.4.14. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.14/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.14/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ip and socks in /webapp/server Removes [ip](https://github.com/indutny/node-ip). It's no longer used after updating ancestor dependency [socks](https://github.com/JoshGlazebrook/socks). These dependencies need to be updated together. Removes `ip` Updates `socks` from 2.7.1 to 2.8.3 - [Release notes](https://github.com/JoshGlazebrook/socks/releases) - [Commits](JoshGlazebrook/socks@2.7.1...2.8.3) --- updated-dependencies: - dependency-name: ip dependency-type: indirect - dependency-name: socks dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Fix bug --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yan Xu <yxu@pn1704854.lanl.gov> Co-authored-by: yxu-lanl <38266469+yxu-lanl@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * SRA download template. updated templates for new config file * comment cleanup * Fix option that didn't need to be exposed in configuration * SRA download automatically detects PE vs SE files and handles appropriately. Updated testing snapshots * Binning (#46) * images updated to bind custom scripts at runtime. started readsBinning workflow * fixed IDBA crash on SE reads * basic read binning done * Report generation (#45) * creating final report and QC images * images and report publishing to output directory. updated test snapshots * allow variable md5 in QC PDF report * updated templates --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yan Xu <yxu@pn1704854.lanl.gov> Co-authored-by: yxu-lanl <38266469+yxu-lanl@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
aw-watson
added a commit
that referenced
this pull request
Mar 26, 2025
* subworkflow from readsTaxonomyAssignment * removed old RTA config * initial conversion of contigsTaxonomyAssignment to subworkflow * bind mounts moved to process directives * fixed default container behavior * connections for RTA fixed * updated Dockerfile * RTA bugfix and rework * validation aligner binds in scripts at read time * integrated contigsTaxonomyAssignment * overhauled flow of provided contig data through pipeline. added annotation * reworked contig file flow. annotation, phagefinder, antismash worked into modules * fix accidental deletion * documented more options in config * Update modules branch (#44) * Add webapp * added example python functions for interacting with Nextflow (#18) * Update nextflow in webapp and add cromwell workflows * Track nextflow job * Move report options from command to config file * Update runFaQCs outdir setting * Update output path to match the workflow name in UI * Update content container width * Update body paddings * Update content container lg width * Uncomment nextflowJobMonitor * Fix bug * Disable prop-type validation * Track pid * Test SRA workflow with cromwell * Disable workflow * Update notification toast * Update env * Update table settings * Update form title * Fix null error * Reimplement ORCiD login * Bump mongoose from 6.12.2 to 6.13.6 in /webapp/server Bumps [mongoose](https://github.com/Automattic/mongoose) from 6.12.2 to 6.13.6. - [Release notes](https://github.com/Automattic/mongoose/releases) - [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md) - [Commits](Automattic/mongoose@6.12.2...6.13.6) --- updated-dependencies: - dependency-name: mongoose dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump path-to-regexp and express in /webapp/server Bumps [path-to-regexp](https://github.com/pillarjs/path-to-regexp) to 0.1.12 and updates ancestor dependency [express](https://github.com/expressjs/express). These dependencies need to be updated together. Updates `path-to-regexp` from 0.1.7 to 0.1.12 - [Release notes](https://github.com/pillarjs/path-to-regexp/releases) - [Changelog](https://github.com/pillarjs/path-to-regexp/blob/master/History.md) - [Commits](pillarjs/path-to-regexp@v0.1.7...v0.1.12) Updates `express` from 4.18.2 to 4.21.2 - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/4.21.2/History.md) - [Commits](expressjs/express@4.18.2...4.21.2) --- updated-dependencies: - dependency-name: path-to-regexp dependency-type: indirect - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump cross-spawn in /webapp/server Bumps and [cross-spawn](https://github.com/moxystudio/node-cross-spawn). These dependencies needed to be updated together. Updates `cross-spawn` from 6.0.5 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) Updates `cross-spawn` from 7.0.3 to 7.0.6 - [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md) - [Commits](moxystudio/node-cross-spawn@v6.0.5...v7.0.6) --- updated-dependencies: - dependency-name: cross-spawn dependency-type: indirect - dependency-name: cross-spawn dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump axios from 1.6.0 to 1.7.9 in /webapp/server Bumps [axios](https://github.com/axios/axios) from 1.6.0 to 1.7.9. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/v1.x/CHANGELOG.md) - [Commits](axios/axios@v1.6.0...v1.7.9) --- updated-dependencies: - dependency-name: axios dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump pug from 3.0.2 to 3.0.3 in /webapp/server Bumps [pug](https://github.com/pugjs/pug) from 3.0.2 to 3.0.3. - [Release notes](https://github.com/pugjs/pug/releases) - [Commits](https://github.com/pugjs/pug/compare/pug@3.0.2...pug@3.0.3) --- updated-dependencies: - dependency-name: pug dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ejs from 3.1.9 to 3.1.10 in /webapp/server Bumps [ejs](https://github.com/mde/ejs) from 3.1.9 to 3.1.10. - [Release notes](https://github.com/mde/ejs/releases) - [Commits](mde/ejs@v3.1.9...v3.1.10) --- updated-dependencies: - dependency-name: ejs dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nodemailer and mailparser in /webapp/server Bumps [nodemailer](https://github.com/nodemailer/nodemailer) to 6.10.0 and updates ancestor dependency [mailparser](https://github.com/nodemailer/mailparser). These dependencies need to be updated together. Updates `nodemailer` from 6.9.7 to 6.10.0 - [Release notes](https://github.com/nodemailer/nodemailer/releases) - [Changelog](https://github.com/nodemailer/nodemailer/blob/master/CHANGELOG.md) - [Commits](nodemailer/nodemailer@v6.9.7...v6.10.0) Updates `mailparser` from 3.6.5 to 3.7.2 - [Release notes](https://github.com/nodemailer/mailparser/releases) - [Changelog](https://github.com/nodemailer/mailparser/blob/master/CHANGELOG.md) - [Commits](nodemailer/mailparser@v3.6.5...v3.7.2) --- updated-dependencies: - dependency-name: nodemailer dependency-type: direct:production - dependency-name: mailparser dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump braces from 3.0.2 to 3.0.3 in /webapp/server Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3. - [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md) - [Commits](micromatch/braces@3.0.2...3.0.3) --- updated-dependencies: - dependency-name: braces dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump nanoid from 3.3.7 to 3.3.8 in /webapp/client Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.7 to 3.3.8. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](ai/nanoid@3.3.7...3.3.8) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Bump vite from 5.4.9 to 5.4.14 in /webapp/client Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 5.4.9 to 5.4.14. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/v5.4.14/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/v5.4.14/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> * Bump ip and socks in /webapp/server Removes [ip](https://github.com/indutny/node-ip). It's no longer used after updating ancestor dependency [socks](https://github.com/JoshGlazebrook/socks). These dependencies need to be updated together. Removes `ip` Updates `socks` from 2.7.1 to 2.8.3 - [Release notes](https://github.com/JoshGlazebrook/socks/releases) - [Commits](JoshGlazebrook/socks@2.7.1...2.8.3) --- updated-dependencies: - dependency-name: ip dependency-type: indirect - dependency-name: socks dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> * Fix bug --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yan Xu <yxu@pn1704854.lanl.gov> Co-authored-by: yxu-lanl <38266469+yxu-lanl@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * SRA download template. updated templates for new config file * comment cleanup * Fix option that didn't need to be exposed in configuration * SRA download automatically detects PE vs SE files and handles appropriately. Updated testing snapshots * Binning (#46) * images updated to bind custom scripts at runtime. started readsBinning workflow * fixed IDBA crash on SE reads * basic read binning done * Report generation (#45) * creating final report and QC images * images and report publishing to output directory. updated test snapshots * allow variable md5 in QC PDF report * updated templates * fix base DB binding * updated custom DB binds * added report generation for contig and read-based taxonomic analysis --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Yan Xu <yxu@pn1704854.lanl.gov> Co-authored-by: yxu-lanl <38266469+yxu-lanl@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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