From f804cd13d986c93ee215951dd5871d171b02c9a9 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 18 Jan 2024 12:57:49 -0800 Subject: [PATCH] Remove references to Nextalign CLI MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Nextalign CLI was removed in Nextclade V3¹ ¹ https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html#nextalign-cli-is-removed --- src/index.rst | 1 - src/learn/parts.rst | 9 ++++----- src/snippets/ambient-setup.rst | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/index.rst b/src/index.rst index 74f26e0b..4c96ad13 100644 --- a/src/index.rst +++ b/src/index.rst @@ -82,7 +82,6 @@ team and other Nextstrain users provide assistance. For private inquiries, Auspice Nextstrain CLI Nextclade CLI - Nextalign CLI nextstrain.org .. toctree:: diff --git a/src/learn/parts.rst b/src/learn/parts.rst index 90ebb644..4a412361 100644 --- a/src/learn/parts.rst +++ b/src/learn/parts.rst @@ -236,11 +236,10 @@ together all of the above to provide a consistent way to run pathogen workflows, access Nextstrain tools like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch, and publish datasets to nextstrain.org. -:doc:`Nextclade ` is a web application and two command-line -programs (``nextclade`` and ``nextalign``) for performing viral genome -alignment, mutation calling, clade assignment, quality checks, and phylogenetic -placement. Nextclade can be used indepedently of other Nextstrain tools as -well as integrated into workflows. +:doc:`Nextclade ` is a web application and a command-line +tool for performing viral genome alignment, mutation calling, clade assignment, +quality checks, and phylogenetic placement. Nextclade can be used independently +of other Nextstrain tools as well as integrated into workflows. With this overview, you'll be better prepared to :doc:`install Nextstrain ` and :doc:`run a workflow ` or :doc:`contribute diff --git a/src/snippets/ambient-setup.rst b/src/snippets/ambient-setup.rst index 56786f6a..dcdd5589 100644 --- a/src/snippets/ambient-setup.rst +++ b/src/snippets/ambient-setup.rst @@ -10,7 +10,7 @@ conda install --override-channels --strict-channel-priority \ -c conda-forge -c bioconda --yes \ - augur auspice nextalign nextclade \ + augur auspice nextclade \ snakemake git epiweeks pangolin pangolearn \ ncbi-datasets-cli