From 2692d2782c18c9ca9d00c5e3cd577edcd096be05 Mon Sep 17 00:00:00 2001
From: Matthew Wells <mattwells9@shaw.ca>
Date: Tue, 22 Oct 2024 15:49:07 -0500
Subject: [PATCH] updated workflow for linting

---
 .github/workflows/linting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index fff238b2..76ea76ec 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -53,7 +53,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}