Merge branch 'dev' into dev_normalization

nf-core · Feb 18, 2025 · afd739e · afd739e
2 parents 33b0ba6 + 7cdc5bf
commit afd739e
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Showing 6 changed files with 68 additions and 26 deletions.
diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/cloudtest.yml
@@ -81,13 +81,24 @@ jobs:
     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/request-action@v2.x
+      - name: Get PR reviews
+        uses: octokit/request-action@v2.x
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
+        continue-on-error: true
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - id: test_variables
+
+      - name: Check for approvals
+        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
+        run: |
+          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
+          exit 1
+
+      - name: Check for enough approvals (>=2)
+        id: test_variables
         if: github.event_name != 'workflow_dispatch'
         run: |
           JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
@@ -114,11 +125,9 @@ jobs:
             }
           profiles: ${{ matrix.profile }}
 
-      - uses: actions/upload-artifact@v3
-        name: Save Logs
-        if: success() || failure()
+      - uses: actions/upload-artifact@v4
         with:
-          name: tower-${{ matrix.profile }}-log
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,15 +9,44 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [1803](https://github.com/nf-core/sarek/pull/1803) - Back to dev
 - [1682](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files; edit vcf_concatenate_germline subworkflow
-- [1760](https://github.com/nf-core/sarek/pull/1760) - Back to dev
+
+### Changed
+
+### Fixed
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
+| Params | Status |
+| ------ | ------ |
+
+## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå
+
+Akkatjåkkå is another glacier.
+
+### Added
+
+- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev
 
 ### Changed
 
 - [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
+- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport
+- [1798](https://github.com/nf-core/sarek/pull/1798) - Prepare release 3.5.1
 
 ### Fixed
 
+- [1797](https://github.com/nf-core/sarek/pull/1797) - Use `file-path-pattern` over `file-path` to hanlde glob for `known_indels` and `known_indels_tbi` to fix [1785](https://github.com/nf-core/sarek/issues/1785)
+- [1802](https://github.com/nf-core/sarek/pull/1802) - Update GHA for full_test tests
+
 ### Removed
 
 ### Dependencies

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,9 +3,10 @@ custom_logo_url: https://github.com/nf-core/sarek/
 custom_logo_title: "nf-core/sarek"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev" target="_blank">nf-core/sarek</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/sarek/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/tree/dev"
+  target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to
+  interpret these results, please see the <a href="https://nf-co.re/sarek/dev/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000
@@ -41,7 +42,8 @@ module_order:
       name: "FastP (Read preprocessing)"
   - picard:
       name: "GATK4 MarkDuplicates"
-      info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)."
+      info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity
+        (with --use_gatk_spark)."
   - samtools:
       name: "Samtools Flagstat"
   - mosdepth:
@@ -63,7 +65,7 @@ extra_fn_clean_exts:
     pattern: "^.*.(md|recal).mosdepth.(global|region).dist"
     module: mosdepth
 
-sample_names_replace_regex: True
+sample_names_replace_regex: true
 sample_names_replace:
   "\\.[0-9]{4}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity
   module: picard

diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config
@@ -16,7 +16,9 @@
 process {
 
     withName: 'GATK4_GENOMICSDBIMPORT' {
-        ext.args   = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
+        ext.args   = { params.wes ?
+                            '--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' :
+                            '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
         ext.prefix = { "${meta.intervals_name}.joint" }
         publishDir = [
             enabled: false

diff --git a/nextflow.config b/nextflow.config
@@ -337,14 +337,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -712,7 +712,7 @@
                 "known_indels": {
                     "type": "string",
                     "fa_icon": "fas fa-copy",
-                    "format": "file-path",
+                    "format": "file-path-pattern",
                     "exists": true,
                     "mimetype": "text/plain",
                     "description": "Path to known indels file.",
@@ -721,7 +721,7 @@
                 "known_indels_tbi": {
                     "type": "string",
                     "fa_icon": "fas fa-copy",
-                    "format": "file-path",
+                    "format": "file-path-pattern",
                     "exists": true,
                     "mimetype": "text/plain",
                     "description": "Path to known indels file index.",