From 8f8d8da9567cc297471ba1102f4514b24741c393 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 18 Jun 2024 01:15:35 +0200 Subject: [PATCH 01/11] fix copypasta --- topics/dev/tutorials/tool-from-scratch/tutorial.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/topics/dev/tutorials/tool-from-scratch/tutorial.md b/topics/dev/tutorials/tool-from-scratch/tutorial.md index 3bbcd56589aac7..4253ea92e2f529 100644 --- a/topics/dev/tutorials/tool-from-scratch/tutorial.md +++ b/topics/dev/tutorials/tool-from-scratch/tutorial.md @@ -433,8 +433,7 @@ anyone wrapping a tool, a more complete list is available in [the Galaxy tool do Planemo is an important tool within the Galaxy development workflow. Although it will be covered in greater detail in the next section of this tutorial, one of its functions is necessary for the tool wrapper development. `planemo` is available -via the python package manager `pip`. To that end, before beginning this section, please install `planemo` locally by running -`planemo`. To that end, before beginning this section, please install planemo locally by running +via the python package manager `pip`. To that end, before beginning this section, please install planemo locally by running > Installing `planemo` via pip > From e4a98f5870a7569e8460f328adfd8e78174799aa Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Mon, 7 Oct 2024 07:47:44 +0000 Subject: [PATCH 02/11] add new recording from Google Form submission --- .../ERGA-post-assembly-QC/tutorial.md | 41 +++++++++++++------ 1 file changed, 28 insertions(+), 13 deletions(-) diff --git a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md index c1eb9cb8a9aa85..e49c8f96e32bf2 100644 --- a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md +++ b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md @@ -1,30 +1,45 @@ --- layout: tutorial_hands_on - title: ERGA post-assembly QC questions: -- "What combination of tools can assess the quality of a genome assembly?" -- "What metrics can help to analyse the quality of an asembly?" -- "How do we evaluate the outputs?" +- What combination of tools can assess the quality of a genome assembly? +- What metrics can help to analyse the quality of an asembly? +- How do we evaluate the outputs? objectives: -- "Apply the post-assembly-QC-workflow using the necessary tools" -- "Analyse and evaluate the results of the workflow" +- Apply the post-assembly-QC-workflow using the necessary tools +- Analyse and evaluate the results of the workflow time_estimation: 3H key_points: -- "The ERGA post-assembly pipeline allows users to assess and improve the quality of genome assemblies" -- "The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination and overview with BlobToolKit, providing analysis information and statistics, and Hi-C scaffolding." +- The ERGA post-assembly pipeline allows users to assess and improve the quality of + genome assemblies +- 'The ERGA post-assembly pipeline consists of three main steps: Genome assembly decontamination + and overview with BlobToolKit, providing analysis information and statistics, and + Hi-C scaffolding.' contributors: - GitFab93 - gallardoalba - tbrown91 tags: - - plants - - animals - - genome - - assembly - - QC +- plants +- animals +- genome +- assembly +- QC +recordings: +- youtube_id: TODO + length: 44M + galaxy_version: 24.1.3.dev0 + date: '2024-10-06' + speakers: + - delphine-l + captioners: + - delphine-l + bot-timestamp: 1728229662 + + --- + ![ERGA logo, 4 colorful letters on white background, with the European star circle](../../images/post-assembly-QC/ERGA.logo.jpg){: width="20px"} The European Reference Genome Atlas ([ERGA](https://www.erga-biodiversity.eu/), {% cite Mazzoni2023 %}) is a large-scale network of researchers aiming to generate high-quality reference genomes for all eukaryotic life in Europe and build capacity to allow researchers anywhere to generate reference genomes and use them to answer questions regarding species conservation and biodiversity. ERGA uses state-of-the-art sequencing technologies and advanced bioinformatics tools to produce high-quality genome assemblies. From 8a1b9bf451014b4074330d629ac37c1f171c62f3 Mon Sep 17 00:00:00 2001 From: teresa-m Date: Mon, 7 Oct 2024 12:24:59 +0200 Subject: [PATCH 03/11] Update topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md --- topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md index e49c8f96e32bf2..29c5539513bf5e 100644 --- a/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md +++ b/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.md @@ -26,7 +26,7 @@ tags: - assembly - QC recordings: -- youtube_id: TODO +- youtube_id: n4PNTTa2d6U length: 44M galaxy_version: 24.1.3.dev0 date: '2024-10-06' From 68773b35f82468030143cbd0a4476b6ce324a751 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 8 Oct 2024 10:50:14 +0200 Subject: [PATCH 04/11] Optimistically handle plausible button --- _layouts/tutorial_hands_on.html | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html index 7573628cd1d611..ae38499d40d824 100644 --- a/_layouts/tutorial_hands_on.html +++ b/_layouts/tutorial_hands_on.html @@ -290,10 +290,13 @@

You've Finished the Tutorial