apply suggestions from code review

nf_core/create.py

@@ -497,7 +497,6 @@ def fix_linting(self):
  # Add the lint content to the preexisting nf-core config
  config_fn, nf_core_yml = nf_core.utils.load_tools_config(self.outdir)
  nf_core_yml["lint"] = lint_config
- print("added linting config")
  with open(self.outdir / config_fn, "w") as fh:
  yaml.dump(nf_core_yml, fh, default_flow_style=False, sort_keys=False)
 

nf_core/lint/files_exist.py

@@ -196,15 +196,12 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
  Path("lib", "Checks.groovy"),
  Path("lib", "Completion.groovy"),
  Path("lib", "Workflow.groovy"),
- ]
- files_warn_ifexists = [
- Path(".travis.yml"),
- Path("lib", "NfcoreTemplate.groovy"),
  Path("lib", "Utils.groovy"),
  Path("lib", "WorkflowMain.groovy"),
  Path("lib", "NfcoreTemplate.groovy"),
  Path("lib", f"Workflow{short_name[0].upper()}{short_name[1:]}.groovy"),
  ]
+ files_warn_ifexists = [Path(".travis.yml")]
  files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
  (Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),
  ]

nf_core/pipeline-template/workflows/pipeline.nf

@@ -65,8 +65,8 @@ workflow {{ short_name|upper }} {
  )
 
  emit:
- multiqc_report = MULTIQC.out.report // channel: /path/to/multiqc_report.html
- versions = ch_versions // channel: [ path(versions.yml) ]
+ multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
+ versions = ch_versions  // channel: [ path(versions.yml) ]
 }
 
 /*