From d1b71a1cb500aa18a0b8713ec98ce0f9cdd0f20a Mon Sep 17 00:00:00 2001
From: Steven Sutcliffe <sgsutcliffe@gmail.com>
Date: Thu, 10 Oct 2024 15:00:31 -0400
Subject: [PATCH] Update lint CLI command

---
 .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 1fcafe8..8b60f35 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -51,7 +51,7 @@ 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() }}