Merge branch 'dev' into documentation

Author: LouisLeNezet

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.0
+    rev: v0.8.1
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -12,11 +12,13 @@
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
 - Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
 - Move `includeConfig 'conf/modules.config'` next to `includeConfig 'conf/base.config'` to not overwrite tests profiles configurations ([#3301](https://github.com/nf-core/tools/pull/3301))
+- Use `params.monochrome_logs` in the template and update nf-core components ([#3310](https://github.com/nf-core/tools/pull/3310))
 - Fix some typos and improve writing in `usage.md` and `CONTRIBUTING.md` ([#3302](https://github.com/nf-core/tools/pull/3302))
 
 ### Download
 
 - First steps towards fixing [#3179](https://github.com/nf-core/tools/issues/3179): Modify `prioritize_direct_download()` to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into `gather_registries()` ([#3244](https://github.com/nf-core/tools/pull/3244)).
+- Update dawidd6/action-download-artifact action to v7 ([#3306](https://github.com/nf-core/tools/pull/3306))
 
 ### Linting
 
@@ -50,6 +52,7 @@
 - Update codecov/codecov-action action to v5 ([#3283](https://github.com/nf-core/tools/pull/3283))
 - Update python:3.12-slim Docker digest to 2a6386a ([#3284](https://github.com/nf-core/tools/pull/3284))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.0 ([#3299](https://github.com/nf-core/tools/pull/3299))
+- Update gitpod/workspace-base Docker digest to 12853f7 ([#3309](https://github.com/nf-core/tools/pull/3309))
 
 ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]
 

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@sha256:2cc134fe5bd7d8fdbe44cab294925d4bc6d2d178d94624f4c376584a22d1f7b6
+FROM gitpod/workspace-base@sha256:12853f7c901eb2b677a549cb112c85f9679d18feb30093bcc63aa252540ecad9
 
 USER root
 

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

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
+        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
         with:
           workflow: linting.yml
           workflow_conclusion: completed

nf_core/pipeline-template/modules.json

@@ -8,7 +8,7 @@
                     {%- if fastqc %}
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
                         "installed_by": ["modules"]
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
@@ -23,17 +23,17 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "9a1e8bb6a5d205cf7807dcefca872a3314b2f3e6",
                         "installed_by": ["subworkflows"]
                     }{% if nf_schema %},
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }{% endif %}
                 }

nf_core/pipeline-template/modules/nf-core/fastqc/main.nf

@@ -41,7 +41,7 @@ params {
     email_on_fail                = null
     plaintext_email              = false
     {%- endif %}
-    {%- if modules %}
+    {%- if modules or nf_schema %}
     monochrome_logs              = false{% endif %}
     {%- if slackreport or adaptivecard %}
     hook_url                     = null{% endif %}
@@ -291,6 +291,7 @@ plugins {
 
 validation {
     defaultIgnoreParams = ["genomes"]
+    monochromeLogs = params.monochrome_logs
     help {
         enabled = true
         command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"

nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml

@@ -182,7 +182,7 @@
                     "fa_icon": "fas fa-file-upload",
                     "hidden": true
                 },{% endif %}
-                {%- if modules %}
+                {%- if modules or nf_schema %}
                 "monochrome_logs": {
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",