diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index d2607dd..8114ae9 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -5,6 +5,8 @@ on: push: branches: [main] +env: + NXF_SYNTAX_PARSER: "v2" jobs: pre-commit: runs-on: ubuntu-latest diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5daf125..6ab6747 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -9,11 +9,12 @@ on: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + NFT_VER: "0.9.3" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + NXF_SYNTAX_PARSER: "v2" jobs: test: runs-on: ubuntu-latest @@ -21,7 +22,7 @@ jobs: matrix: JAVA_VERSION: ["17", "21"] NXF_VER: - - "24.10.5" + - "25.10.0" - "latest-everything" steps: diff --git a/tests/filterNextflowOutput/main.nf b/tests/filterNextflowOutput/main.nf index c0a257a..0909aae 100644 --- a/tests/filterNextflowOutput/main.nf +++ b/tests/filterNextflowOutput/main.nf @@ -1,14 +1,14 @@ include { FASTQC } from './modules/local/fastqc' -params.failure = false -params.outdir = "results" -params.monochrome_logs = false +params { + failure : Boolean = false + outdir : String = "results" + monochrome_logs : Boolean = false +} workflow { - - colors = getColors(params.monochrome_logs) - - input = channel.of( + def colors = getColors(params.monochrome_logs) + def input = channel.of( 'sample_1', 'sample_2', 'sample_3', diff --git a/tests/getAllFilesFromDir/main.nf b/tests/getAllFilesFromDir/main.nf index 42cec9b..6f2f840 100644 --- a/tests/getAllFilesFromDir/main.nf +++ b/tests/getAllFilesFromDir/main.nf @@ -1,5 +1,4 @@ workflow { - def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') // stable_content diff --git a/tests/getRelativePath/main.nf b/tests/getRelativePath/main.nf index 42cec9b..6f2f840 100644 --- a/tests/getRelativePath/main.nf +++ b/tests/getRelativePath/main.nf @@ -1,5 +1,4 @@ workflow { - def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') // stable_content diff --git a/tests/removeNextflowVersion/main.nf b/tests/removeNextflowVersion/main.nf index d0b1320..8088f48 100644 --- a/tests/removeNextflowVersion/main.nf +++ b/tests/removeNextflowVersion/main.nf @@ -1,5 +1,4 @@ workflow { - channel.of( """ Workflow: