From 71935a9c3cea1968b41c9fe7bbf4ac433dced0a3 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Wed, 21 Jan 2026 12:11:42 +0100 Subject: [PATCH 1/2] nextflow lint --- .github/workflows/lint.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 7476c6166c15..8b11069b14cd 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -157,6 +157,9 @@ jobs: - name: Lint module ${{ matrix.module }} run: nf-core modules lint ${{ matrix.module }} + - name: Nextflow lint module ${{ matrix.module }} + run: export NXF_SYNTAX_PARSER=v2; nextflow lint modules/nf-core/${{ matrix.module }} + nf-core-lint-subworkflows: runs-on: - runs-on=${{ github.run_id }}-nf-core-lint-subworkflows @@ -189,6 +192,9 @@ jobs: - name: Lint subworkflow ${{ matrix.subworkflow }} run: nf-core subworkflows lint ${{ matrix.subworkflow }} + - name: Nextflow lint subworkflow ${{ matrix.subworkflow }} + run: export NXF_SYNTAX_PARSER=v2; nextflow lint subworkflows/nf-core/${{ matrix.subworkflow }} + confirm-pass-lint: runs-on: - runs-on=${{ github.run_id }}-confirm-pass-lint From 2e424958c546e45059e4074bcf63e9db691d0043 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 21 Jan 2026 12:14:43 +0100 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: Phil Ewels --- .github/workflows/lint.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 8b11069b14cd..77d42a656a36 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -158,7 +158,7 @@ jobs: run: nf-core modules lint ${{ matrix.module }} - name: Nextflow lint module ${{ matrix.module }} - run: export NXF_SYNTAX_PARSER=v2; nextflow lint modules/nf-core/${{ matrix.module }} + run: NXF_SYNTAX_PARSER=v2 nextflow lint modules/nf-core/${{ matrix.module }} nf-core-lint-subworkflows: runs-on: @@ -193,7 +193,7 @@ jobs: run: nf-core subworkflows lint ${{ matrix.subworkflow }} - name: Nextflow lint subworkflow ${{ matrix.subworkflow }} - run: export NXF_SYNTAX_PARSER=v2; nextflow lint subworkflows/nf-core/${{ matrix.subworkflow }} + run: NXF_SYNTAX_PARSER=v2 nextflow lint subworkflows/nf-core/${{ matrix.subworkflow }} confirm-pass-lint: runs-on: