diff --git a/nf_core/create.py b/nf_core/create.py index fa900cdb06..c094d33a22 100644 --- a/nf_core/create.py +++ b/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) diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py index 3e98526266..5d62a23bf8 100644 --- a/nf_core/lint/files_exist.py +++ b/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"}), ] diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index f7de301ce5..68adbaa328 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/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) ] } /*