Merge branch 'dev' into use-integrated-pdiff

Author: mashehu

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.11.11
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -13,6 +13,9 @@
 - run nf-test tests on runsOn runners ([#3525](https://github.com/nf-core/tools/pull/3525))
 - 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))
+- Do not skip AWS fulltest action on release ([#3583](https://github.com/nf-core/tools/pull/3583))
 
 ### Linting
 
@@ -80,6 +83,7 @@
 - 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 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]
 

nf_core/modules/lint/environment_yml.py

@@ -83,7 +83,28 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
 
         if valid_env_yml:
             # Check that the dependencies section is sorted alphabetically
-            if sorted(env_yml["dependencies"]) == env_yml["dependencies"]:
+            def sort_recursively(obj):
+                """Simple recursive sort for nested structures."""
+                if isinstance(obj, list):
+
+                    def get_key(x):
+                        if isinstance(x, dict):
+                            # For dicts like {"pip": [...]}, use the key "pip"
+                            return (list(x.keys())[0], 1)
+                        else:
+                            # For strings like "pip=23.3.1", use "pip" and for bioconda::samtools=1.15.1, use "bioconda::samtools"
+                            return (str(x).split("=")[0], 0)
+
+                    return sorted([sort_recursively(item) for item in obj], key=get_key)
+                elif isinstance(obj, dict):
+                    return {k: sort_recursively(v) for k, v in obj.items()}
+                else:
+                    return obj
+
+            sorted_dependencies = sort_recursively(env_yml["dependencies"])
+
+            # Direct comparison of sorted vs original dependencies
+            if sorted_dependencies == env_yml["dependencies"]:
                 module.passed.append(
                     (
                         "environment_yml_sorted",
@@ -96,6 +117,6 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
                 log.info(
                     f"Dependencies in {module.component_name}'s environment.yml were not sorted alphabetically. Sorting them now."
                 )
-                env_yml["dependencies"].sort()
+                env_yml["dependencies"] = sorted_dependencies
                 with open(Path(module.component_dir, "environment.yml"), "w") as fh:
                     yaml.dump(env_yml, fh, Dumper=custom_yaml_dumper())

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == '{{ name }}' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable

nf_core/pipeline-template/conf/base.config

@@ -15,7 +15,7 @@ process {
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 

nf_core/pipeline-template/nextflow.config

@@ -83,7 +83,9 @@ process {
     memory = { 6.GB * task.attempt }
     time   = { 4.h  * task.attempt }
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    // 175 signals that the Pipeline had an unrecoverable error while
+    // restoring a Snapshot via Fusion Snapshots.
+    errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 }
@@ -304,7 +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 {

requirements.txt

@@ -7,7 +7,6 @@ jsonschema>=4.0
 markdown>=3.3
 packaging
 pillow
-pdiff
 pre-commit
 prompt_toolkit<=3.0.51
 pydantic>=2.2.1