Merge pull request #1681 from nf-core/nf-core-template-merge-3.0.1

Important! Template update for nf-core/tools v3.0.1

.editorconfig

@@ -11,7 +11,6 @@ indent_style = space
 [*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset
@@ -26,12 +25,9 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
-
-
 [/assets/email*]
 indent_size = unset
 
-
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset

.github/CONTRIBUTING.md

@@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 

.github/workflows/cloudtest.yml

@@ -1,8 +1,13 @@
-name: nf-core cloud test
+name: nf-core cloud full size tests
+# This workflow is triggered on PRs opened against the master branch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
+# It runs the -profile 'test_full' on cloud
 
 on:
   release:
     types: [created]
+  pull_request_review:
+    types: [submitted]
   workflow_dispatch:
     inputs:
       test:
@@ -31,10 +36,7 @@ on:
         default: true
 
 jobs:
-  trigger-test:
-    name: launch
-    runs-on: ubuntu-latest
-    if: ${{ github.repository == 'nf-core/sarek' }}
+  run-platform:
     strategy:
       fail-fast: false
       matrix:
@@ -74,10 +76,26 @@ jobs:
             cloud: aws
             compute_env: TOWER_COMPUTE_ENV
             workdir: TOWER_BUCKET_AWS
-
+    name: Run AWS full tests
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/sarek' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
     steps:
+      - uses: octokit/[email protected]
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+
       # Launch workflow on AWS Batch
-      - name: Launch
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false
         # If is false, we negate and run the job

.nf-core.yml

@@ -7,19 +7,17 @@ lint:
     - conf/modules.config
   files_unchanged:
     - .gitignore
-    - .github/workflows/linting.yml
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png
   modules_config: false
   template_strings: false
-nf_core_version: 3.0.0
+nf_core_version: 3.0.1
 org_path: null
 repository_type: pipeline
 template:
   author: Maxime Garcia, Szilveszter Juhos, Friederike Hanssen
-  description: An open-source analysis pipeline to detect germline or somatic variants
-    from whole genome or targeted sequencing
+  description: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
   force: false
   is_nfcore: true
   name: sarek

.prettierignore

@@ -1,4 +1,3 @@
-
 email_template.html
 adaptivecard.json
 slackreport.json

CHANGELOG.md

@@ -18,16 +18,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
+- [1680](https://github.com/nf-core/sarek/pull/1680) - Template update for nf-core/tools v3.0.0
+- [1681](https://github.com/nf-core/sarek/pull/1681) - Template update for nf-core/tools v3.0.1
 
 ### Fixed
 
-- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
 - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
 - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests
 - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge
 
 ### Removed
 
+- [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
+
 ### Dependencies
 
 | Dependency    | Old version | New version |
@@ -42,10 +45,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Params          | Status  |
-| --------------- | ------- |
-| `snpeff_db`     | Updated |
-| `snpeff_genome` | Removed |
+| Params                               | Status  |
+| ------------------------------------ | ------- |
+| `--help_full`                        | New     |
+| `--show_hidden`                      | New     |
+| `--snpeff_db`                        | Updated |
+| `--snpeff_genome`                    | Removed |
+| `--validationFailUnrecognisedParams` | Removed |
+| `--validationLenientMode`            | Removed |
+| `--validationSchemaIgnoreParams`     | Removed |
+| `--validationShowHiddenParams`       | Removed |
 
 ## [3.4.4](https://github.com/nf-core/sarek/releases/tag/3.4.4) - Ruopsokjåkhå
 

modules.json

@@ -515,12 +515,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
+                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
+                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

nextflow.config

@@ -10,6 +10,7 @@ params {
     // Workflow flags:
 
     // Mandatory arguments
+    // Input options
     input         = null      // No default input
     input_restart = null      // No default automatic input
     step          = 'mapping' // Starts with mapping
@@ -120,10 +121,10 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+
     // Config options
     config_profile_name        = null
     config_profile_description = null
-
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null

subworkflows/local/utils_nfcore_sarek_pipeline/main.nf

@@ -23,9 +23,9 @@ include { samplesheetToList         } from 'plugin/nf-schema'
 include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW TO INITIALISE PIPELINE
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_INITIALISATION {
@@ -166,9 +166,9 @@ if (params.tools && (params.tools.split(',').contains('vep')    || params.tools.
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUBWORKFLOW FOR PIPELINE COMPLETION
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
 workflow PIPELINE_COMPLETION {
@@ -214,9 +214,9 @@ workflow PIPELINE_COMPLETION {
 }
 
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     FUNCTIONS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 //
 // Check and validate pipeline parameters