From 7fdd8d9c2f23a41614d506243d5662cf38cc94d7 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 6 Dec 2024 15:39:40 -0800 Subject: [PATCH 1/2] phylogenetic/nextclade: Add links to tutorials and zika/mpox repos --- nextclade/README.md | 8 ++++++++ phylogenetic/README.md | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/nextclade/README.md b/nextclade/README.md index e3f99e7..620591c 100644 --- a/nextclade/README.md +++ b/nextclade/README.md @@ -6,6 +6,14 @@ The new standard would be to include the Nextclade workflow within the pathogen This workflow is used to create the Nextclade datasets for this pathogen. All official Nextclade datasets are available at https://github.com/nextstrain/nextclade_data. +> [!IMPORTANT] +> We do not have a generalized nextclade workflow so the rules files are empty and +> will need to be filled in with your own rules. We suggest that you go through the +> [Nextclade dataset create guide](https://github.com/nextstrain/nextclade_data/blob/@/docs/dataset-creation-guide.md) +> to understand how to create a Nextclade dataset from scratch. Then use +> [mpox](https://github.com/nextstrain/mpox) as an example to create your own +> nextclade workflow. + ## Workflow Usage The workflow can be run from the top level pathogen repo directory: diff --git a/phylogenetic/README.md b/phylogenetic/README.md index 7e961c8..daba241 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -3,6 +3,14 @@ This workflow uses metadata and sequences to produce one or multiple [Nextstrain datasets][] that can be visualized in Auspice. +> [!IMPORTANT] +> We do not have a generalized phylogenetic workflow so the rules files are empty and +> will need to be filled in with your own rules. We suggest that you go through the +> [Create a phylogenetic workflow tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html) +> to understand the simplified zika-tutorial workflow. Then use [zika](https://github.com/nextstrain/zika) +> and [mpox](https://github.com/nextstrain/mpox) as examples to create +> your own phylogenetic workflow. + ## Workflow Usage The workflow can be run from the top level pathogen repo directory: From 1bde98e1956306e879fd4d239bc8c6344e5d6b59 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Mon, 9 Dec 2024 11:51:51 -0800 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: John SJ Anderson --- nextclade/README.md | 4 ++-- phylogenetic/README.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nextclade/README.md b/nextclade/README.md index 620591c..fc8b393 100644 --- a/nextclade/README.md +++ b/nextclade/README.md @@ -9,10 +9,10 @@ All official Nextclade datasets are available at https://github.com/nextstrain/n > [!IMPORTANT] > We do not have a generalized nextclade workflow so the rules files are empty and > will need to be filled in with your own rules. We suggest that you go through the -> [Nextclade dataset create guide](https://github.com/nextstrain/nextclade_data/blob/@/docs/dataset-creation-guide.md) +> [Nextclade dataset creation guide](https://github.com/nextstrain/nextclade_data/blob/@/docs/dataset-creation-guide.md) > to understand how to create a Nextclade dataset from scratch. Then use > [mpox](https://github.com/nextstrain/mpox) as an example to create your own -> nextclade workflow. +> Nextclade workflow. ## Workflow Usage diff --git a/phylogenetic/README.md b/phylogenetic/README.md index daba241..fd2ef87 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -6,7 +6,7 @@ that can be visualized in Auspice. > [!IMPORTANT] > We do not have a generalized phylogenetic workflow so the rules files are empty and > will need to be filled in with your own rules. We suggest that you go through the -> [Create a phylogenetic workflow tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html) +> ["Creating a phylogenetic workflow" tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html) > to understand the simplified zika-tutorial workflow. Then use [zika](https://github.com/nextstrain/zika) > and [mpox](https://github.com/nextstrain/mpox) as examples to create > your own phylogenetic workflow.