Merge pull request #2278 from adamrtalbot/catch_modules_with_quay.io

Linting error if quay.io found in biocontainer name

CHANGELOG.md

@@ -12,6 +12,7 @@
 ### Linting
 
 - Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270))
+- Error if module container specification has quay.io as prefix when it shouldn't have ([#2278])(https://github.com/nf-core/tools/pull/2278/files)
 - Detect if container is 'simple name' and try to contact quay.io server by default ([#2281](https://github.com/nf-core/tools/pull/2281))
 
 ### Modules

nf_core/modules/lint/main_nf.py

@@ -271,15 +271,7 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.failed.append(("singularity_tag", "Unable to parse singularity tag", self.main_nf))
                 singularity_tag = None
             url = urlparse(l.split("'")[0])
-            # lint double quotes
-            if l.count('"') > 2:
-                self.failed.append(
-                    (
-                        "container_links",
-                        "Too many double quotes found when specifying singularity container",
-                        self.main_nf,
-                    )
-                )
+
         if _container_type(l) == "docker":
             # e.g. "quay.io/biocontainers/krona:2.7.1--pl526_5' }" -> 2.7.1--pl526_5
             # e.g. "biocontainers/biocontainers:v1.2.0_cv1' }" -> v1.2.0_cv1
@@ -289,23 +281,44 @@ def check_process_section(self, lines, fix_version, progress_bar):
                 self.passed.append(("docker_tag", f"Found docker tag: {docker_tag}", self.main_nf))
             else:
                 self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
-                docker_tag = None
+                docker_tag = NoneD
+            if l.startswith("quay.io/"):
+                l_stripped = re.sub("\W+$", "", l)
+                self.failed.append(
+                    (
+                        "container_links",
+                        f"{l_stripped} container name found, please use just 'organisation/container:tag' instead.",
+                        self.main_nf,
+                    )
+                )
+            else:
+                self.passed.append(("container_links", f"Container prefix is correct", self.main_nf))
+
             # Guess if container name is simple one (e.g. nfcore/ubuntu:20.04)
             # If so, add quay.io as default container prefix
             if l.count("/") == 1 and l.count(":") == 1:
                 l = "quay.io/" + l
             url = urlparse(l.split("'")[0])
-            # lint double quotes
-            if l.count('"') > 2:
-                self.failed.append(
-                    ("container_links", "Too many double quotes found when specifying docker container", self.main_nf)
-                )
+
         # lint double quotes
-        if l.startswith("container"):
+        if l.startswith("container") or _container_type(l) == "docker" or _container_type(l) == "singularity":
             if l.count('"') > 2:
                 self.failed.append(
-                    ("container_links", "Too many double quotes found when specifying containers", self.main_nf)
+                    (
+                        "container_links",
+                        f"Too many double quotes found when specifying container: {l.lstrip('container ')}",
+                        self.main_nf,
+                    )
                 )
+            else:
+                self.passed.append(
+                    (
+                        "container_links",
+                        f"Correct number of double quotes found when specifying container: {l.lstrip('container ')}",
+                        self.main_nf,
+                    )
+                )
+
         # lint more than one container in the same line
         if ("https://containers" in l or "https://depot" in l) and ("biocontainers/" in l or "quay.io/" in l):
             self.warned.append(

tests/modules/patch.py

@@ -18,7 +18,7 @@
 """
 
 ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2"
-CORRECT_SHA = "0245a9277d51a47c8aa68d264d294cf45312fab8"
+CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f"
 SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e"
 FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73"
 BISMARK_ALIGN = "bismark/align"