Merge pull request #2263 from mashehu/fix-template-modules

Update template modules
nf-core · Apr 28, 2023 · fe2c5e8 · fe2c5e8
2 parents 9f9e588 + 95d7ef3
commit fe2c5e8
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Showing 8 changed files with 22 additions and 22 deletions.
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -403,7 +403,7 @@ def check_process_labels(self, lines):
     if len(all_labels) > 0:
         for label in all_labels:
             try:
-                label = re.match("^label\s+([a-zA-Z0-9_-]+)$", label).group(1)
+                label = re.match(r"^label\s+'?([a-zA-Z0-9_-]+)'?$", label).group(1)
             except AttributeError:
                 self.warned.append(
                     (

diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
@@ -17,7 +17,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/nf_core/pipeline-template/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/...ne-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/...ne-template/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
@@ -122,7 +122,7 @@ def __init__(self):
 
 PROCESS_LABEL_GOOD = (
     """
-    label process_high
+    label 'process_high'
     cpus 12
     """,
     1,
@@ -131,7 +131,7 @@ def __init__(self):
 )
 PROCESS_LABEL_NON_ALPHANUMERIC = (
     """
-    label a:label:with:colons
+    label 'a:label:with:colons'
     cpus 12
     """,
     0,
@@ -140,8 +140,8 @@ def __init__(self):
 )
 PROCESS_LABEL_GOOD_CONFLICTING = (
     """
-    label process_high
-    label process_low
+    label 'process_high'
+    label 'process_low'
     cpus 12
     """,
     0,
@@ -150,8 +150,8 @@ def __init__(self):
 )
 PROCESS_LABEL_GOOD_DUPLICATES = (
     """
-    label process_high
-    label process_high
+    label 'process_high'
+    label 'process_high'
     cpus 12
     """,
     0,
@@ -160,8 +160,8 @@ def __init__(self):
 )
 PROCESS_LABEL_GOOD_AND_NONSTANDARD = (
     """
-    label process_high
-    label process_extra_label
+    label 'process_high'
+    label 'process_extra_label'
     cpus 12
     """,
     1,
@@ -170,7 +170,7 @@ def __init__(self):
 )
 PROCESS_LABEL_NONSTANDARD = (
     """
-    label process_extra_label
+    label 'process_extra_label'
     cpus 12
     """,
     0,