From 49abb1434b96a60e1e9c8ead7167cf3025abcc7a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 Oct 2025 12:23:33 +0100 Subject: [PATCH 1/3] use v2 of syntax for 25 --- .github/workflows/pre-commit.yml | 2 ++ tests/filterNextflowOutput/main.nf | 14 +++++++------- tests/getAllFilesFromDir/main.nf | 1 - tests/getRelativePath/main.nf | 1 - tests/removeNextflowVersion/main.nf | 1 - 5 files changed, 9 insertions(+), 10 deletions(-) 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/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: From 8276cf7205b907b11fbd51ce4c768c11af073c8e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 Oct 2025 12:33:19 +0100 Subject: [PATCH 2/3] bump minimal NF version --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5daf125..a336af8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -9,7 +9,7 @@ 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 @@ -21,7 +21,7 @@ jobs: matrix: JAVA_VERSION: ["17", "21"] NXF_VER: - - "24.10.5" + - "25.10.0" - "latest-everything" steps: From a302a36606c1446995ce21714dd7808b70227478 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 Oct 2025 12:47:36 +0100 Subject: [PATCH 3/3] v2 in tests too --- .github/workflows/test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a336af8..6ab6747 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,6 +14,7 @@ env: 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