From 9e2054e2baa005c8020e168c9631d47ff9d07c14 Mon Sep 17 00:00:00 2001 From: Geert van Geest Date: Fri, 8 Apr 2022 10:08:46 +0200 Subject: [PATCH 1/3] tries to add bioschemas --- docs/index.md | 24 ++++++++++++++++++++++++ mkdocs.yml | 1 + overrides/main.html | 10 ++++++++++ 3 files changed, 35 insertions(+) diff --git a/docs/index.md b/docs/index.md index 40c9c5d..299660e 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 3117d00..cbe4bcd 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -28,6 +28,7 @@ edit_uri: edit/main/docs/ site_url: https://sib-swiss.github.io/NGS-variants-training/ markdown_extensions: + - meta - abbr - def_list - footnotes diff --git a/overrides/main.html b/overrides/main.html index ff188f3..0b35273 100644 --- a/overrides/main.html +++ b/overrides/main.html @@ -12,3 +12,13 @@ gtag('config', 'G-SK9D4D2P4M'); {% endblock %} + +{% block extrahead %} + {% if page and page.meta and page.meta.bioschemas %} + + {% else %} + + {% endif %} +{% endblock %} From 5b9497ddb33b5d68cf27b8dede151b736d1aad04 Mon Sep 17 00:00:00 2001 From: Geert van Geest Date: Tue, 10 Jan 2023 09:02:13 +0100 Subject: [PATCH 2/3] changes position of favicon --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index af18196..61e9af2 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 From 5864b5ab1b305f57ee96f24ead886f0ece2db1ad Mon Sep 17 00:00:00 2001 From: Geert van Geest Date: Thu, 9 Feb 2023 15:16:18 +0100 Subject: [PATCH 3/3] updates docker base image --- Docker/Dockerfile | 2 +- docs/assets/schemas.json | 53 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 docs/assets/schemas.json 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