[rdjsonl] reported by reviewdog 🐶 You have skipped a heading level, please correct this. <details><summary>Listing of Heading Levels</summary> ``` # Important terms to know # VGP assembly pipeline overview # Get data ### HiFi reads preprocessing with **cutadapt** # Genome profile analysis ## Generation of _k_-mer spectra with **Meryl** ## Genome profiling with **GenomeScope2** # Assembly with **hifiasm** ## Assembly evaluation ## HiC-phased assembly with **hifiasm** ## Pseudohaplotype assembly with **hifiasm** ## Purging the primary and alternate assemblies ### Parsing **purge_dups** cutoffs from **GenomeScope2** output ## Purging with **purge_dups** ### Read-depth analysis ### Generation of all versus all self-alignment ### Resolution of haplotigs and overlaps ### Process the alternate assembly ### Post-purge quality control # Scaffolding # Hybrid scaffolding with Bionano optical maps ## Evaluating Bionano scaffolds # Hi-C scaffolding ### Pre-processing Hi-C data ### Generate initial Hi-C contact map ### SALSA2 scaffolding ### Evaluate the final genome assembly with Pretext # Conclusion ``` </details> Raw Output: {"message":"You have skipped a heading level, please correct this.\n<details><summary>Listing of Heading Levels</summary>\n\n```\n# Important terms to know\n# VGP assembly pipeline overview\n# Get data\n### HiFi reads preprocessing with **cutadapt**\n# Genome profile analysis\n## Generation of _k_-mer spectra with **Meryl**\n## Genome profiling with **GenomeScope2**\n# Assembly with **hifiasm**\n## Assembly evaluation\n## HiC-phased assembly with **hifiasm**\n## Pseudohaplotype assembly with **hifiasm**\n## Purging the primary and alternate assemblies\n### Parsing **purge_dups** cutoffs from **GenomeScope2** output\n## Purging with **purge_dups**\n### Read-depth analysis\n### Generation of all versus all self-alignment\n### Resolution of haplotigs and overlaps\n### Process the alternate assembly\n### Post-purge quality control\n# Scaffolding\n# Hybrid scaffolding with Bionano optical maps\n## Evaluating Bionano scaffolds\n# Hi-C scaffolding\n### Pre-processing Hi-C data\n### Generate initial Hi-C contact map\n### SALSA2 scaffolding\n### Evaluate the final genome assembly with Pretext\n# Conclusion\n```\n</details>","location":{"path":"./topics/assembly/tutorials/vgp_genome_assembly/tutorial.md","range":{"start":{"line":196,"column":1},"end":{"line":196,"column":4}}},"severity":"ERROR","code":{"value":"GTN:028","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn028"},"suggestions":[{"text":"##","range":{"start":{"line":196,"column":1},"end":{"line":196,"column":4}}}]}

[rdjsonl] reported by reviewdog 🐶 You have skipped a heading level, please correct this. <details><summary>Listing of Heading Levels</summary> ``` # Important terms to know # VGP assembly pipeline overview # Get data ### HiFi reads preprocessing with **cutadapt** # Genome profile analysis ## Generation of _k_-mer spectra with **Meryl** ## Genome profiling with **GenomeScope2** # Assembly with **hifiasm** ## Assembly evaluation ## HiC-phased assembly with **hifiasm** ## Pseudohaplotype assembly with **hifiasm** ## Purging the primary and alternate assemblies ### Parsing **purge_dups** cutoffs from **GenomeScope2** output ## Purging with **purge_dups** ### Read-depth analysis ### Generation of all versus all self-alignment ### Resolution of haplotigs and overlaps ### Process the alternate assembly ### Post-purge quality control # Scaffolding # Hybrid scaffolding with Bionano optical maps ## Evaluating Bionano scaffolds # Hi-C scaffolding ### Pre-processing Hi-C data ### Generate initial Hi-C contact map ### SALSA2 scaffolding ### Evaluate the final genome assembly with Pretext # Conclusion ``` </details> Raw Output: {"message":"You have skipped a heading level, please correct this.\n<details><summary>Listing of Heading Levels</summary>\n\n```\n# Important terms to know\n# VGP assembly pipeline overview\n# Get data\n### HiFi reads preprocessing with **cutadapt**\n# Genome profile analysis\n## Generation of _k_-mer spectra with **Meryl**\n## Genome profiling with **GenomeScope2**\n# Assembly with **hifiasm**\n## Assembly evaluation\n## HiC-phased assembly with **hifiasm**\n## Pseudohaplotype assembly with **hifiasm**\n## Purging the primary and alternate assemblies\n### Parsing **purge_dups** cutoffs from **GenomeScope2** output\n## Purging with **purge_dups**\n### Read-depth analysis\n### Generation of all versus all self-alignment\n### Resolution of haplotigs and overlaps\n### Process the alternate assembly\n### Post-purge quality control\n# Scaffolding\n# Hybrid scaffolding with Bionano optical maps\n## Evaluating Bionano scaffolds\n# Hi-C scaffolding\n### Pre-processing Hi-C data\n### Generate initial Hi-C contact map\n### SALSA2 scaffolding\n### Evaluate the final genome assembly with Pretext\n# Conclusion\n```\n</details>","location":{"path":"./topics/assembly/tutorials/vgp_genome_assembly/tutorial.md","range":{"start":{"line":1194,"column":1},"end":{"line":1194,"column":4}}},"severity":"ERROR","code":{"value":"GTN:028","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn028"},"suggestions":[{"text":"##","range":{"start":{"line":1194,"column":1},"end":{"line":1194,"column":4}}}]}

Process completed with exit code 1.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions/setup-python@v2, actions/cache@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

[rdjsonl] reported by reviewdog 🐶 Instead of embedding IFrames to YouTube contents, consider adding this video to the [GTN Video Library](https://github.com/gallantries/video-library/issues/) where it will be more visible for others. Raw Output: {"message":"Instead of embedding IFrames to YouTube contents, consider adding this video to the [GTN Video Library](https://github.com/gallantries/video-library/issues/) where it will be more visible for others.","location":{"path":"./faqs/galaxy/workflows_import_from_dockstore.md","range":{"start":{"line":29,"column":21},"end":{"line":29,"column":289}}},"severity":"WARNING","code":{"value":"GTN:002","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn002"},"suggestions":[{"text":"","range":{"start":{"line":29,"column":21},"end":{"line":29,"column":289}}}]}

[rdjsonl] reported by reviewdog 🐶 Instead of embedding IFrames to YouTube contents, consider adding this video to the [GTN Video Library](https://github.com/gallantries/video-library/issues/) where it will be more visible for others. Raw Output: {"message":"Instead of embedding IFrames to YouTube contents, consider adding this video to the [GTN Video Library](https://github.com/gallantries/video-library/issues/) where it will be more visible for others.","location":{"path":"./faqs/galaxy/workflows_import_from_url.md","range":{"start":{"line":27,"column":21},"end":{"line":27,"column":289}}},"severity":"WARNING","code":{"value":"GTN:002","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn002"},"suggestions":[{"text":"","range":{"start":{"line":27,"column":21},"end":{"line":27,"column":289}}}]}