diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index a0beb23636..9f3fbdd90f 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -63,7 +63,7 @@ jobs:
         run: |
           git config --global user.email "core@nf-co.re"
           git config --global user.name "nf-core-bot"
-          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync nf-core/${{ matrix.pipeline }} \
+          nf-core --log-file sync_log_${{ matrix.pipeline }}.txt sync -d nf-core/${{ matrix.pipeline }} \
             --from-branch dev \
             --pull-request \
             --username nf-core-bot \
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 062e885d95..6686a728d1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,15 @@
 # nf-core/tools: Changelog
 
+## [v2.0.1 - Palladium Platypus Junior](https://github.com/nf-core/tools/releases/tag/2.0.1) - [2021-07-13]
+
+### Template
+
+* Critical tweak to add `--dir` declaration to `nf-core lint` GitHub Actions `linting.yml` workflow
+
+### General
+
+* Add `--dir` declaration to `nf-core sync` GitHub Actions `sync.yml` workflow
+
 ## [v2.0 - Palladium Platypus](https://github.com/nf-core/tools/releases/tag/2.0) - [2021-07-13]
 
 ### :warning: Major enhancements & breaking changes
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 5a99efb260..afe4197c38 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -127,7 +127,7 @@ 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 ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}
diff --git a/setup.py b/setup.py
index 686c011e96..4f16b75a60 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = "2.0"
+version = "2.0.1"
 
 with open("README.md") as f:
     readme = f.read()