Merge branch 'dev' into use-integrated-pdiff

Author: mashehu

.github/workflows/nextflow-source-test.yml

@@ -70,8 +70,7 @@ jobs:
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
           AWS_DEFAULT_REGION: "eu-west-1"
         with:
-          # to: nextflow-nightly-test-aaaaqbupbi4ikkrdg6b3bemnoq@nfcore.slack.com
-          to: [email protected]
+          to: ${{ secrets.NEXTFLOW_NIGHTLY_NOTIFICATION_EMAIL_ADDRESS }}
           from: [email protected]
           subject: "Nextflow source test CI failed"
           body: |

CHANGELOG.md

@@ -79,10 +79,13 @@
 - Dev ([#3557](https://github.com/nf-core/tools/pull/3557))
 - chore(deps): update python:3.12-slim docker digest to bae1a06 ([#3558](https://github.com/nf-core/tools/pull/3558))
 - Update CI to test template pipelines with nf-test ([#3559](https://github.com/nf-core/tools/pull/3559))
+- Use secret for notification email on nextflow nightly builds ([#3576](https://github.com/nf-core/tools/pull/3576))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.9 ([#3563](https://github.com/nf-core/tools/pull/3563))
 - chore(deps): update python:3.12-slim docker digest to 31a416d ([#3568](https://github.com/nf-core/tools/pull/3568))
 - chore(deps): update codecov/codecov-action digest to 18283e0 ([#3575](https://github.com/nf-core/tools/pull/3575))
 - use pdiff from setup-nf-test ([#3578](https://github.com/nf-core/tools/pull/3578))
+- chore(deps): update python:3.12-slim docker digest to fd95fa2 ([#3587](https://github.com/nf-core/tools/pull/3587))
+- chore(deps): update gitpod/workspace-base docker digest to 3aa18f4 ([#3586](https://github.com/nf-core/tools/pull/3586))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.11 ([#3585](https://github.com/nf-core/tools/pull/3585))
 
 ## [v3.2.1 - Pewter Pangolin Patch](https://github.com/nf-core/tools/releases/tag/3.2.1) - [2025-04-29]

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:31a416db24bd8ade7dac5fd5999ba6c234d7fa79d4add8781e95f41b187f4c9a
+FROM python:3.12-slim@sha256:fd95fa221297a88e1cf49c55ec1828edd7c5a428187e67b5d1805692d11588db
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

nf_core/__main__.py

@@ -2080,7 +2080,7 @@ def command_bump_version(ctx, new_version, directory, nextflow):
 @click.pass_context
 def command_list(ctx, keywords, sort, json, show_archived):
     """
-    DEPREUse `nf-core pipelines list` instead.CATED
+    Use `nf-core pipelines list` instead.
     """
     log.warning(
         "The `[magenta]nf-core list[/]` command is deprecated. Use `[magenta]nf-core pipelines list[/]` instead."

nf_core/gitpod/gitpod.Dockerfile

@@ -2,7 +2,7 @@
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base@sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6
+FROM gitpod/workspace-base@sha256:3aa18f4fbebc6ee2017a223463fa86af7e8c757d27a6542272d4c6ab6ab3fdaa
 
 USER root