Merge branch 'dev' into snapshot-exit-code

Author: mirpedrol

.github/workflows/pytest.yml

@@ -194,7 +194,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5
+      - uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5
         with:
           files: coverage.xml
         env:

CHANGELOG.md

@@ -14,6 +14,7 @@
 - Include the centralized nf-core configs also in offline mode, if a local copy is available. ([#3491](https://github.com/nf-core/tools/pull/3491))
 - downgrade nf-schema to fix CI tests ([#3544](https://github.com/nf-core/tools/pull/3544))
 - Make jobs automatically resubmit for exit code 175 ([#3564](https://github.com/nf-core/tools/pull/3564))
+- bump nf-schema back to 2.3.0 ([#3577](https://github.com/nf-core/tools/pull/3577))
 
 ### Linting
 
@@ -64,7 +65,7 @@
 - Changing retrieval of file extension from EDAM ([#3512](https://github.com/nf-core/tools/pull/3512))
 - Refactor adding EDAM ontologies and allowing detect more patterns (e.g., versions.yml) ([#3519](https://github.com/nf-core/tools/pull/3519))
 - Add offline configs test action ([#3524](https://github.com/nf-core/tools/pull/3524))
-- Adds `test-datasets` subcommand for listing/searching files in the nf-core/test-datasets repo from the cli ([#3487](https://github.com/nf-core/tools/issues/3487), [#3548](https://github.com/nf-core/tools/pull/3548))
+- Adds `test-datasets` subcommand for listing/searching files in the nf-core/test-datasets repo from the cli ([#3487](https://github.com/nf-core/tools/issues/3487), [#3548](https://github.com/nf-core/tools/pull/3548), [#3566](https://github.com/nf-core/tools/pull/3566), [#3567](https://github.com/nf-core/tools/pull/3567))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.11.2 ([#3521](https://github.com/nf-core/tools/pull/3521))
 - Fix indentation in included_configs API docs ([#3523](https://github.com/nf-core/tools/pull/3523))
 - chore(deps): update python:3.12-slim docker digest to a866731 ([#3527](https://github.com/nf-core/tools/pull/3527))
@@ -78,6 +79,8 @@
 - 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))
 - 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))
 
 ## [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:bae1a061b657f403aaacb1069a7f67d91f7ef5725ab17ca36abc5f1b2797ff92
+FROM python:3.12-slim@sha256:31a416db24bd8ade7dac5fd5999ba6c234d7fa79d4add8781e95f41b187f4c9a
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

nf_core/pipeline-template/nextflow.config

@@ -306,7 +306,7 @@ manifest {
 {% if nf_schema -%}
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

nf_core/test_datasets/list.py

@@ -73,11 +73,11 @@ def list_datasets(
     else:
         table = rich.table.Table()
         if generate_nf_path:
-            table.add_column("Nextflow Import")
+            table.add_column("Nextflow Import", overflow="fold")
         elif generate_dl_url:
-            table.add_column("Download URL")
+            table.add_column("Download URL", overflow="fold")
         else:
-            table.add_column("File")
+            table.add_column("File", overflow="fold")
 
         for el in out:
             table.add_row(el)

nf_core/test_datasets/search.py

@@ -67,6 +67,8 @@ def search_datasets(
         stdout.print(create_download_url(branch, selection))
     else:
         table = rich.table.Table(show_header=False)
+        table.add_column("")
+        table.add_column("", overflow="fold")
         table.add_row("File Name:", selection)
         table.add_row("Nextflow Import:", create_pretty_nf_path(selection, branch == MODULES_BRANCH_NAME))
         table.add_row("Download Link:", create_download_url(branch, selection))