Merge pull request #1462 from drpatelh/fixes

Run nf-core create manually and fix YAMLLint
nf-core · Mar 16, 2022 · 9675b24 · 9675b24
2 parents 0a70779 + 9176ef4
commit 9675b24
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Showing 10 changed files with 95 additions and 89 deletions.
diff --git a/nf_core/pipeline-template/.github/workflows/awsfulltest.yml b/nf_core/pipeline-template/.github/workflows/awsfulltest.yml
@@ -18,7 +18,7 @@ jobs:
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
-        {% raw %}
+        {%- raw %}
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

diff --git a/nf_core/pipeline-template/.github/workflows/awstest.yml b/nf_core/pipeline-template/.github/workflows/awstest.yml
@@ -12,7 +12,7 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        {% raw %}
+        {%- raw %}
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

diff --git a/nf_core/pipeline-template/.github/workflows/branch.yml b/nf_core/pipeline-template/.github/workflows/branch.yml
@@ -43,4 +43,4 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-{% endraw %}
+{%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -138,4 +138,4 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
-{% endraw %}
+{%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting_comment.yml b/nf_core/pipeline-template/.github/workflows/linting_comment.yml
@@ -1,4 +1,4 @@
-{% raw %}
+{% raw -%}
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +27,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-{% endraw %}
+{%- endraw %}
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -7,10 +7,10 @@
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "multiqc": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             }
         }
     }

diff --git a/nf_core/pipeline-template/modules/nf-core/modules/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/modules/fastqc/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/modules/fastqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/modules/fastqc/meta.yml
diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/modules/multiqc/meta.yml