Fix outdated fix message in lint

nf-core · Aug 9, 2021 · 4a4d821 · 4a4d821
1 parent 0129101
commit 4a4d821
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 * Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
 * Fixed bug in `nf-core launch` due to revisions specified with `-r` not being added to nextflow command. ([#1246](https://github.com/nf-core/tools/issues/1246))
+* Update 'fix' message in `nf-core lint` to conform to the current command line options. ([#1259](https://github.com/nf-core/tools/issues/1259))
 
 ### Modules
 

diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
@@ -38,7 +38,9 @@ def print_fixes(lint_obj, module_lint_obj):
     """Prints available and applied fixes"""
 
     if len(lint_obj.could_fix):
-        fix_cmd = "nf-core lint {} --fix {}".format(lint_obj.wf_path, " --fix ".join(lint_obj.could_fix))
+        fix_cmd = "nf-core lint {}--fix {}".format(
+            "" if lint_obj.wf_path == "." else f"--dir {lint_obj.wf_path}", " --fix ".join(lint_obj.could_fix)
+        )
         console.print(
             f"\nTip: Some of these linting errors can automatically be resolved with the following command:\n\n[blue]    {fix_cmd}\n"
         )