From a9ce08000edd6fb1a7abb6d2a81d68b55106df59 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:01:59 -0700 Subject: [PATCH 1/3] Reference new top-level name in CI build target --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 1af597d..a8bd5c6 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -8,4 +8,4 @@ jobs: ci: uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master with: - build-args: auspice/flu_avian_h5n1_ha.json + build-args: auspice/avian-flu_h5n1_ha.json From f8df5fff2cd2eedc7dcea44b8fc971865b1b02ce Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:02:58 -0700 Subject: [PATCH 2/3] Reference new top-level name in AWS Batch script --- batch.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/batch.py b/batch.py index bccabf7..825ba3e 100644 --- a/batch.py +++ b/batch.py @@ -30,8 +30,8 @@ for segment in params.segments: call = ['nextstrain', 'build', '--aws-batch', '.', '-j 1'] targets = [] - targets.append('auspice/flu_avian_%s_%s_tree.json'%(subtype, segment)) - targets.append('auspice/flu_avian_%s_%s_meta.json'%(subtype, segment)) + targets.append('auspice/avian-flu_%s_%s_tree.json'%(subtype, segment)) + targets.append('auspice/avian-flu_%s_%s_meta.json'%(subtype, segment)) call.extend(targets) print(' '.join(call)) log = open('logs/%s_%s.txt'%(subtype, segment), 'w') From cb887f6fe69831005607af6ae0f05fbacf332aa1 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Fri, 19 Apr 2024 11:05:43 -0700 Subject: [PATCH 3/3] Reference new top-level name in quickstart build --- quickstart-build/Snakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/quickstart-build/Snakefile b/quickstart-build/Snakefile index 3c9cf6f..bb18d24 100755 --- a/quickstart-build/Snakefile +++ b/quickstart-build/Snakefile @@ -15,7 +15,7 @@ SEGMENTS = ["ha"] generated JSON files in the auspice folder for each subtype and segment.""" rule all: input: - auspice_json = expand("auspice/flu_avian_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS) + auspice_json = expand("auspice/avian-flu_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS) """Specify all input files here. For this build, you'll start with input sequences from the example_data folder, which contain metadata information in the @@ -305,7 +305,7 @@ rule export: node_data = node_data_by_wildcards, auspice_config = files.auspice_config output: - auspice_json = "auspice/flu_avian_{subtype}_{segment}.json" + auspice_json = "auspice/avian-flu_{subtype}_{segment}.json" shell: """ augur export v2 \