From 0a208ab250dbebd47dfad94793dc83c7b3db8b5b Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 8 Dec 2025 10:49:05 -0800
Subject: [PATCH 1/2] Sync scheduled workflows list

Some new scheduled workflows have been added since this list was last
updated.

The list was generated programmatically using:

    gh api "search/code?q=org:nextstrain+path:.github/workflows+schedule&per_page=100" | \
    jq -r '.items[] | "          - { repo: \(.repository.name),\(" " * (16 - (.repository.name | length)))workflow: \(.name) }"' | \
    LC_ALL=C sort -f
---
 .github/workflows/keep-workflows-enabled.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/keep-workflows-enabled.yaml b/.github/workflows/keep-workflows-enabled.yaml
index ddcdbdc..f3f0d22 100644
--- a/.github/workflows/keep-workflows-enabled.yaml
+++ b/.github/workflows/keep-workflows-enabled.yaml
@@ -24,10 +24,12 @@ jobs:
           - { repo: .github,         workflow: keep-workflows-enabled.yaml }
           - { repo: augur,           workflow: ci.yaml }
           - { repo: avian-flu,       workflow: ingest-to-phylogenetic-ncbi.yaml }
+          - { repo: chikv,           workflow: fetch-and-ingest.yaml }
           - { repo: cli,             workflow: ci.yaml }
           - { repo: cli,             workflow: standalone-installers.yaml }
           - { repo: conda-base,      workflow: installation.yaml }
           - { repo: dengue,          workflow: ingest-to-phylogenetic.yaml }
+          - { repo: ebola,           workflow: ci.yaml }
           - { repo: forecasts-ncov,  workflow: run-usa-models.yaml }
           - { repo: forecasts-ncov,  workflow: update-ncov-case-counts.yaml }
           - { repo: hmpv,            workflow: ingest.yaml }
@@ -38,7 +40,6 @@ jobs:
           - { repo: mumps,           workflow: ingest.yaml }
           - { repo: ncov,            workflow: rebuild-100k.yml }
           - { repo: ncov-ingest,     workflow: fetch-and-ingest-genbank-master.yml }
-          - { repo: ncov-ingest,     workflow: fetch-and-ingest-gisaid-master.yml }
           - { repo: nextclade_data,  workflow: update-sars-cov-2-datasets.yml }
           - { repo: nextstrain.org,  workflow: index-resources.yml }
           - { repo: nextstrain.org,  workflow: remind-to-promote.yml }
@@ -53,6 +54,7 @@ jobs:
           - { repo: seasonal-cov,    workflow: ingest.yaml }
           - { repo: seasonal-flu,    workflow: run-private-nextflu-builds.yaml }
           - { repo: status,          workflow: ci.yaml }
+          - { repo: tb,              workflow: ingest-to-phylogenetic.yaml }
           - { repo: WNV,             workflow: ci.yaml }
           - { repo: WNV,             workflow: ingest-to-phylogenetic.yaml }
           - { repo: yellow-fever,    workflow: ingest.yaml }

From 8ca64161bfdff6ec18e251b340f5637266eba0a1 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 8 Dec 2025 10:52:31 -0800
Subject: [PATCH 2/2] Disable all workflows before enabling
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The last user that enabled a disabled workflow or updated the schedule is the one
that "owns" all the future scheduled runs of that workflow and receives any email
notifications if configured in the user's settings.¹

This makes nextstrain-bot the owner of all the workflows listed here,
not just the ones that were automatically disabled due to inactivity.

¹ https://docs.github.com/en/actions/concepts/workflows-and-actions/notifications-for-workflow-runs
---
 .github/workflows/keep-workflows-enabled.yaml | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/keep-workflows-enabled.yaml b/.github/workflows/keep-workflows-enabled.yaml
index f3f0d22..fa89e00 100644
--- a/.github/workflows/keep-workflows-enabled.yaml
+++ b/.github/workflows/keep-workflows-enabled.yaml
@@ -1,6 +1,9 @@
-# This workflow is intended to keep scheduled GH Action workflows enabled
-# as a work-around for scheduled workflows being automatically disabled when
-# no repository activity has occurred in 60 days.
+# This workflow regularly disables and re-enables scheduled GH Action workflows.
+# Reasons:
+# 1. Ensures that email notifications for scheduled runs are configurable by the
+#    team under nextstrain-bot's account settings.
+# 2. Prevents workflows from being automatically disabled when no repository
+#    activity has occurred in 60 days.
 name: Keep workflows enabled
 
 on:
@@ -62,7 +65,16 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - run: |
+      - name: Disable workflow
+        run: |
+          gh api \
+          --method PUT \
+          -H "Accept: application/vnd.github+json" \
+          -H "X-GitHub-Api-Version: 2022-11-28" \
+          /repos/nextstrain/${{matrix.repo}}/actions/workflows/${{matrix.workflow}}/disable
+
+      - name: Enable workflow
+        run: |
           gh api \
           --method PUT \
           -H "Accept: application/vnd.github+json" \