handles doi.org resolver + comments

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -244,10 +244,13 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     // Pipeline DOI
     if (meta.manifest_map.doi) {
+        // Using a loop to handle multiple DOIs
+        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+        // Removing ` ` since the manifest.doi is a string and not a proper list
         def temp_doi_ref = ""
-        String[] manifest_doi = meta.manifest_map.doi.split(",")
-        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref}\'>${doi_ref}</a>), "
-        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length()-2)
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
     } else meta["doi_text"] = ""
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"