Merge branch 'dev' into no_env_in_download_action

.gitpod.yml

@@ -1,4 +1,4 @@
-image: nfcore/gitpod:latest
+image: nfcore/gitpod:dev
 tasks:
   - name: install current state of nf-core/tools and setup pre-commit
     command: |

CHANGELOG.md

@@ -1,5 +1,23 @@
 # nf-core/tools: Changelog
 
+## v3.1.1dev
+
+### Template
+
+### Download
+
+### Linting
+
+### Modules
+
+- fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
+
+### Subworkflows
+
+### General
+
+### Version updates
+
 ## [v3.1.0 - Brass Boxfish](https://github.com/nf-core/tools/releases/tag/3.1.0) - [2024-12-09]
 
 **Highlights**

nf_core/pipeline-template/nextflow.config

@@ -77,11 +77,6 @@ params {
 includeConfig 'conf/base.config'
 {%- else %}
 
-{% if modules -%}
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-{%- endif %}
-
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -336,3 +331,8 @@ validation {
     }{% endif %}
 }
 {%- endif %}
+
+{% if modules -%}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+{%- endif %}

nf_core/pipelines/bump_version.py

@@ -128,8 +128,9 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
         yaml_key=["template", "version"],
     )
 
-    # update rocrate
-    ROCrate(pipeline_obj.wf_path).update_rocrate()
+    # update rocrate if ro-crate is present
+    if Path(pipeline_obj.wf_path, "ro-crate-metadata.json").exists():
+        ROCrate(pipeline_obj.wf_path).update_rocrate()
 
 
 def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None:

nf_core/utils.py

@@ -1083,7 +1083,7 @@ def get_repo_releases_branches(pipeline, wfs):
             raise AssertionError(f"Not able to find pipeline '{pipeline}'")
 
     # Get branch information from github api - should be no need to check if the repo exists again
-    branch_response = gh_api.safe_get(f"https://api.github.com/repos/{pipeline}/branches")
+    branch_response = gh_api.safe_get(f"https://api.github.com/repos/{pipeline}/branches?per_page=100")
     for branch in branch_response.json():
         if (
             branch["name"] != "TEMPLATE"

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.1.0"
+version = "3.1.1dev"
 
 with open("README.md") as f:
     readme = f.read()