diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5553430d3c1f667b2dc0462cf709859df1b1d903..8a623a848e9853b8157e7686d05bff1ba0e21353 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['20.04.0', '']
+        nxf_ver: ['20.04.0', '21.03.0-edge']
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 58e281df6ec884a17db31160853ca23d4ed160f1..fcde400cedbc1566f84e8a811e0b45a1c113df60 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -19,6 +19,34 @@ jobs:
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Markdown linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `markdownlint-cli`
+                * On Mac: `brew install markdownlint-cli`
+                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
+            * Fix the markdown errors
+                * Automatically: `markdownlint . --config .github/markdownlint.yml --fix`
+                * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   YAML:
     runs-on: ubuntu-latest
     steps:
@@ -29,7 +57,34 @@ jobs:
       - name: Install yaml-lint
         run: npm install -g yaml-lint
       - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml")
+        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml")
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## YAML linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `yaml-lint`
+                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Fix the markdown errors
+                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
+                * Fix any reported errors in your YAML files
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+
+
   nf-core:
     runs-on: ubuntu-latest
     steps:
diff --git a/Dockerfile b/Dockerfile
index cae5c2fbc7756b73a8fe90fbe8b2eb6796fc7b08..c6b88ef0af89a2e07519a9aa0958291b7a193ee1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM nfcore/base:1.13.1
+FROM nfcore/base:1.13.2
 LABEL authors="Nicolas Servant" \
       description="Docker image containing all software requirements for the nf-core/hic pipeline"
 
diff --git a/bin/markdown_to_html.py b/bin/markdown_to_html.py
old mode 100644
new mode 100755
diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py
old mode 100644
new mode 100755
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
index 78e8c65d7f2f45b8b503cfeca4aa83b2e22b7404..54935ec818dec805f6d11f90083681589525183b 100644
--- a/lib/NfcoreSchema.groovy
+++ b/lib/NfcoreSchema.groovy
@@ -219,7 +219,7 @@ class NfcoreSchema {
                     }
                 }
             }
-            if(rawSchema.keySet().contains('properties') && rawSchema.get('properties').containsKey(ignore_param)) {
+            if(rawSchema.keySet().contains('properties') && rawSchema.get('properties').keySet().contains(ignore_param)) {
                 rawSchema.get("properties").remove(ignore_param)
             }
             if(rawSchema.keySet().contains('required') && rawSchema.required.contains(ignore_param)) {