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Merge with master@00a53b97 [ci fast]
2 parents 4101ad9 + 00a53b9 commit 71fa033

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.github/workflows/build.yml

+1-21
Original file line numberDiff line numberDiff line change
@@ -52,22 +52,7 @@ jobs:
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echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT
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fi
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- name: Get changed files
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id: changed-files
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uses: tj-actions/changed-files@v43
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with:
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files_ignore: docs/**
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- name: List all changed files
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env:
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ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
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run: |
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for file in ${ALL_CHANGED_FILES}; do
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echo "$file was changed"
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done
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- name: Setup env
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if: steps.changed-files.outputs.any_changed == 'true'
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run: |
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rm -f $HOME/.gitconfig;
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mkdir -p "$HOME/.nextflow";
@@ -76,7 +61,6 @@ jobs:
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NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
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- name: Setup Java ${{ matrix.java_version }}
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if: steps.changed-files.outputs.any_changed == 'true'
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uses: actions/setup-java@v4
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with:
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java-version: ${{matrix.java_version}}
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cache: gradle
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- name: Compile
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if: steps.changed-files.outputs.any_changed == 'true'
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run: make assemble
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- name: Test
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if: steps.changed-files.outputs.any_changed == 'true'
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run: |
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env | sort
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# configure test env
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- name: Publish tests report
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uses: actions/upload-artifact@v4
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if: steps.changed-files.outputs.any_changed == 'true' && always()
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with:
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name: report-unit-tests-jdk-${{ matrix.java_version }}
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path: |
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**/build/reports/tests/test
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outputs:
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any_changed: ${{ steps.changed-files.outputs.any_changed }}
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commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
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test:
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if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
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if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') }}
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needs: build
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runs-on: ubuntu-latest
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timeout-minutes: 90

modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy

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Original file line numberDiff line numberDiff line change
@@ -174,22 +174,6 @@ abstract class BaseScript extends Script implements ExecutionContext {
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if( !entryFlow ) {
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if( meta.getLocalWorkflowNames() )
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throw new AbortOperationException("No entry workflow specified")
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if( meta.getLocalProcessNames() ) {
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final msg = """\
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=============================================================================
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= WARNING =
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= You are running this script using DSL2 syntax, however it does not =
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= contain any 'workflow' definition so there's nothing for Nextflow to run. =
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= =
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= If this script was written using Nextflow DSL1 syntax, please add the =
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= setting 'nextflow.enable.dsl=1' to the nextflow.config file or use the =
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= command-line option '-dsl1' when running the pipeline. =
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= =
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= More details at this link: https://www.nextflow.io/docs/latest/dsl2.html =
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=============================================================================
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""".stripIndent(true)
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throw new AbortOperationException(msg)
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}
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return result
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}
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