Fixed linting errors

HoffLab · Apr 29, 2024 · 3b9edfe · 3b9edfe
1 parent ff79d97
commit 3b9edfe
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Showing 16 changed files with 1,228 additions and 6 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,5 +1,8 @@
 lint:
+  actions_ci: false
   files_exist:
+    - conf/modules.config
+    - conf/test_full.config
     - CODE_OF_CONDUCT.md
     - assets/nf-core-biobakerymgx_logo_light.png
     - docs/images/nf-core-biobakerymgx_logo_light.png
@@ -9,6 +12,9 @@ lint:
     - .github/workflows/awsfulltest.yml
     - conf/igenomes.config
   files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/CONTRIBUTING.md
+    - .github/workflows/linting.yml
     - CODE_OF_CONDUCT.md
     - assets/nf-core-biobakerymgx_logo_light.png
     - docs/images/nf-core-biobakerymgx_logo_light.png

diff --git a/modules.json b/modules.json
@@ -23,17 +23,20 @@
                     "metaphlan/makedb": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/metaphlan/makedb/metaphlan-makedb.diff"
                     },
                     "metaphlan/mergemetaphlantables": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/metaphlan/mergemetaphlantables/metaphlan-mergemetaphlantables.diff"
                     },
                     "metaphlan/metaphlan": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/metaphlan/metaphlan/metaphlan-metaphlan.diff"
                     },
                     "multiqc": {
                         "branch": "master",

diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml