diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/cloudtest.yml index 932951b07c..1015130875 100644 --- 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 index 3e23d4c1d3..1e070216df 100644 --- 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 index ce1a6e388e..814aef8e1d 100644 --- 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 nf-core/sarek - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/sarek analysis pipeline. For information about how to + interpret these results, please see the documentation. 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}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity module: picard diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config index 61a296721d..b3f5bffc8b 100644 --- a/conf/modules/joint_germline.config +++ b/conf/modules/joint_germline.config @@ -16,7 +16,9 @@ process { withName: 'GATK4_GENOMICSDBIMPORT' { - ext.args = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' } + ext.args = { params.wes ? + '--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' : + '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' } ext.prefix = { "${meta.intervals_name}.joint" } publishDir = [ enabled: false diff --git a/nextflow.config b/nextflow.config index b847d21f47..c799ad8a88 100644 --- 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 index f416eeeff9..5f70252f6b 100644 --- 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.",