diff --git a/Docker/Dockerfile b/Docker/Dockerfile index 85e7374..6ed7686 100644 --- a/Docker/Dockerfile +++ b/Docker/Dockerfile @@ -1,4 +1,4 @@ -FROM linuxserver/code-server:4.5.1 +FROM linuxserver/code-server:4.9.1 # Install base utilities RUN apt-get update && \ diff --git a/docs/assets/schemas.json b/docs/assets/schemas.json new file mode 100644 index 0000000..dcd4628 --- /dev/null +++ b/docs/assets/schemas.json @@ -0,0 +1,53 @@ +{ + "@context": "https://schema.org/", + "@type": "LearningResource", + "@id": "https://sib-swiss.github.io/NGS-variants-training", + "http://purl.org/dc/terms/conformsTo": { + "@type": "CreativeWork", + "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE" + }, + "description": "Course on detecting variants from next generation sequencing data", + "keywords": "NGS, variant, SNP, INDEL, sequencing, SNV, gatk", + "name": "NGS - variant analysis", + "about": [ + { + "@type": "DefinedTerm", + "@id": "http://edamontology.org/topic_3168", + "inDefinedTermSet": "http://edamontology.org", + "termCode": "topic_3168", + "name": "Sequencing" + }, + { + "@type": "DefinedTerm", + "@id": "http://edamontology.org/topic_3227", + "inDefinedTermSet": "http://edamontology.org", + "termCode": "topic_3227", + "name": "Variant calling" + } + ], + "abstract": "The detection of genetic variation is of major interest in various disciplines spanning from ecology and evolution research to inherited disease discovery and precision oncology. Next generation sequencing (NGS) methods are very powerful for the detection of genomic variants. Thanks to its throughput and cost-efficiency it enables the detection of a large number of variants in a large number of samples. In this two-day course we will cover the steps from read alignment to variant calling and annotation. We will mainly focus on the detection of germline mutations by following the GATK best practices. ", + "audience": "Biologists working with NGS data", + "author": [ + { + "@type": "Person", + "name": "Geert van Geest", + "email": "geert.vangeest@sib.swiss" + }, + { + "@type": "Person", + "name": "Patricia Palagi" + }, + { + "@type": "Organization", + "name": "SIB Swiss Institute of Bioinformatics" + } + ], + "identifier": "https://doi.org/10.5281/zenodo.6457818", + "license": "https://creativecommons.org/licenses/by/4.0/", + "teaches": [ + "Understand important aspects of NGS and read alignment for variant analysis", + "Perform a read alignment ready for variant analysis", + "Perform variant calling according to GATK best practices", + "Perform a variant annotation" + ] +} \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index bdc4719..3b54f36 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,3 +1,27 @@ +--- +bioschemas: + "@context": https://schema.org/ + "@type": LearningResource + "http://purl.org/dc/terms/conformsTo": + - "@type": CreativeWork + "@id": "https://bioschemas.org/profiles/TrainingMaterial/0.9-DRAFT-2020_12_08/" + about: + - "@id": https://schema.org + - "@id": http://edamontology.org/topic_0089 + audience: + - "@type": Audience + name: (Markup provider, Markup consumer) WebMaster + name: "Adding Schema.org to your website" + author: ["Fred Dibnah", "Niall Beard"] + contributor: + - "@type": Person + name: "Frank Spencer" + description: "In order to establish higher search results for online resources." + keywords: "schemaorg, TeSS" + license: CC-BY 4.0 + version: 1.0 +--- + ## Teachers - Geert van Geest [:custom-orcid:](https://orcid.org/0000-0002-1561-078X) diff --git a/mkdocs.yml b/mkdocs.yml index af18196..09913d1 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -20,10 +20,10 @@ nav: theme: name: material logo: assets/images/SIB_logo.svg + favicon: assets/images/SIB_logo.svg custom_dir: overrides icon: repo: fontawesome/brands/github - favicon: assets/images/SIB_logo.svg features: - announce.dismiss @@ -35,6 +35,7 @@ edit_uri: edit/main/docs/ site_url: https://sib-swiss.github.io/NGS-variants-training/ markdown_extensions: + - meta - abbr - def_list - footnotes