[rdjsonl] reported by reviewdog 🐶 You have skipped a heading level, please correct this. <details><summary>Listing of Heading Levels</summary> ``` # The goal: *E. coli* C-1 assembly # Background on data and tools ## The data ### Illumina data ### Oxford Nanopore Data ## The tools ### Assembly #### Spades ##### Multisized deBruijn graph ##### Read pair utilization ##### Error correction #### Pilon ### Annotation # Let's try it ## Load data and assess quality ### Assess Read Quality ## Assembly with Unicycler ## Assess Assembly quality with Quast ## Annotation with Prokka ## Visualize the results in IGV #### Starting IGV ``` </details> Raw Output: {"message":"You have skipped a heading level, please correct this.\n<details><summary>Listing of Heading Levels</summary>\n\n```\n# The goal: *E. coli* C-1 assembly\n# Background on data and tools\n## The data\n### Illumina data\n### Oxford Nanopore Data\n## The tools\n### Assembly\n#### Spades\n##### Multisized deBruijn graph\n##### Read pair utilization\n##### Error correction\n#### Pilon\n### Annotation\n# Let's try it\n## Load data and assess quality\n### Assess Read Quality\n## Assembly with Unicycler\n## Assess Assembly quality with Quast\n## Annotation with Prokka\n## Visualize the results in IGV\n#### Starting IGV\n```\n</details>","location":{"path":"./topics/assembly/tutorials/unicycler-assembly/tutorial.md","range":{"start":{"line":272,"column":1},"end":{"line":272,"column":5}}},"severity":"ERROR","code":{"value":"GTN:028","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn028"},"suggestions":[{"text":"###","range":{"start":{"line":272,"column":1},"end":{"line":272,"column":5}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not use 'here' as your link title, it is [bad for accessibility](https://usability.yale.edu/web-accessibility/articles/links#link-text). Instead try restructuring your sentence to have useful descriptive text in the link. Raw Output: {"message":"Please do not use 'here' as your link title, it is [bad for accessibility](https://usability.yale.edu/web-accessibility/articles/links#link-text). Instead try restructuring your sentence to have useful descriptive text in the link.","location":{"path":"./topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md","range":{"start":{"line":30,"column":688},"end":{"line":30,"column":694}}},"severity":"ERROR","code":{"value":"GTN:005","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn005"},"suggestions":[{"text":"[Something better here]","range":{"start":{"line":30,"column":688},"end":{"line":30,"column":694}}}]}

[rdjsonl] reported by reviewdog 🐶 You have skipped a heading level, please correct this. <details><summary>Listing of Heading Levels</summary> ``` # Logic # Example history # Practice ## Step 1: Pick a gene and select genomes to analyze ## Step 2: Get amino acid translations for all exons of my gene of interest ## Step 3: Identify and upload genomes of interest ### Uploading sample data ### Uploading VGP data from GenomeArk ### Combine uploaded sequences into a dataset collection ## Step 4: Extract amino acid sequences and genome coordinates for all ORFs ### Extract ORFs from genomic sequences ### Creating __Diamond__ database ## Steps 5, 6, and 7: Finding matches and building trees ## Step 7: Looking at the trees ## Step 8: Generating and interpreting the comparative genome graph ### Starting notebook ### Proving data # Paste link to the dataset here ### Interpreting the graphs # About the gene ``` </details> Raw Output: {"message":"You have skipped a heading level, please correct this.\n<details><summary>Listing of Heading Levels</summary>\n\n```\n# Logic\n# Example history\n# Practice\n## Step 1: Pick a gene and select genomes to analyze\n## Step 2: Get amino acid translations for all exons of my gene of interest\n## Step 3: Identify and upload genomes of interest\n### Uploading sample data\n### Uploading VGP data from GenomeArk\n### Combine uploaded sequences into a dataset collection\n## Step 4: Extract amino acid sequences and genome coordinates for all ORFs\n### Extract ORFs from genomic sequences\n### Creating __Diamond__ database\n## Steps 5, 6, and 7: Finding matches and building trees\n## Step 7: Looking at the trees\n## Step 8: Generating and interpreting the comparative genome graph\n### Starting notebook\n### Proving data\n# Paste link to the dataset here\n### Interpreting the graphs\n# About the gene\n```\n</details>","location":{"path":"./topics/genome-annotation/tutorials/gene-centric/tutorial.md","range":{"start":{"line":355,"column":1},"end":{"line":355,"column":4}}},"severity":"ERROR","code":{"value":"GTN:028","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn028"},"suggestions":[{"text":"##","range":{"start":{"line":355,"column":1},"end":{"line":355,"column":4}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-function/tutorial.md","range":{"start":{"line":63,"column":3},"end":{"line":63,"column":20}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Pretreatments","range":{"start":{"line":63,"column":3},"end":{"line":63,"column":20}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-function/tutorial.md","range":{"start":{"line":96,"column":3},"end":{"line":96,"column":38}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Download metaQuantome Databases","range":{"start":{"line":96,"column":3},"end":{"line":96,"column":38}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-function/tutorial.md","range":{"start":{"line":137,"column":3},"end":{"line":137,"column":38}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Create metaQuantome sample file","range":{"start":{"line":137,"column":3},"end":{"line":137,"column":38}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-function/tutorial.md","range":{"start":{"line":160,"column":3},"end":{"line":160,"column":23}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Run metaQuantome","range":{"start":{"line":160,"column":3},"end":{"line":160,"column":23}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-function/tutorial.md","range":{"start":{"line":265,"column":3},"end":{"line":265,"column":26}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Visualize your Data","range":{"start":{"line":265,"column":3},"end":{"line":265,"column":26}}}]}

[rdjsonl] reported by reviewdog 🐶 Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them. Raw Output: {"message":"Please do not bold headings, it is unncessary and will potentially cause screen readers to shout them.","location":{"path":"./topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md","range":{"start":{"line":61,"column":3},"end":{"line":61,"column":20}}},"severity":"ERROR","code":{"value":"GTN:029","url":"https://github.com/galaxyproject/training-material/wiki/Error-Codes#gtn029"},"suggestions":[{"text":"Pretreatments","range":{"start":{"line":61,"column":3},"end":{"line":61,"column":20}}}]}

reviewdog: Too many results (annotations) in diff. You may miss some annotations due to GitHub limitation for annotation created by logging command. Please check GitHub Actions log console to see all results. Limitation: - 10 warning annotations and 10 error annotations per step - 50 annotations per job (sum of annotations from all the steps) - 50 annotations per run (separate from the job annotations, these annotations aren't created by users) Source: https://github.community/t5/GitHub-Actions/Maximum-number-of-annotations-that-can-be-created-using-GitHub/m-p/39085