Merge pull request #2121 from mirpedrol/dev

allow specifying only one container

CHANGELOG.md

@@ -8,6 +8,8 @@
 
 ### Linting
 
+- Allow specifying containers in less than three lines ([#2121](https://github.com/nf-core/tools/pull/2121))
+
 ### Modules
 
 ### Subworkflows

nf_core/modules/lint/main_nf.py

@@ -271,6 +271,15 @@ 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
@@ -282,13 +291,26 @@ def check_process_section(self, lines, fix_version, progress_bar):
  self.failed.append(("docker_tag", "Unable to parse docker tag", self.main_nf))
  docker_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 docker container", self.main_nf)
+ )
  # lint double quotes
  if l.startswith("container"):
- container_section = l + lines[i + 1] + lines[i + 2]
- if container_section.count('"') > 2:
+ if l.count('"') > 2:
  self.failed.append(
  ("container_links", "Too many double quotes found when specifying containers", 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(
+ (
+ "container_links",
+ "Docker and Singularity containers specified in the same line. Only first one checked.",
+ self.main_nf,
+ )
+ )
  # Try to connect to container URLs
  if url is None:
  continue