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Handle Multiple DOIs from manifest #2946

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merged 6 commits into from
May 3, 2024
Merged

Handle Multiple DOIs from manifest #2946

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b63087e
fix(template): fix handling of multiple DOIs in manifest
maxulysse May 2, 2024
70c191d
Merge branch 'dev' into multiple_DOI
maxulysse May 2, 2024
13e5170
Update nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipe…
maxulysse May 2, 2024
f382f98
handles doi.org resolver + comments
maxulysse May 2, 2024
fa0b60d
update CHANGELOG
maxulysse May 2, 2024
0a9746a
Merge branch 'dev' into multiple_DOI
maxulysse May 3, 2024
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9 changes: 7 additions & 2 deletions nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
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Expand Up @@ -243,8 +243,13 @@ def methodsDescriptionText(mqc_methods_yaml) {
meta["manifest_map"] = workflow.manifest.toMap()

// Pipeline DOI
meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
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>"
if (meta.manifest_map.doi) {
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)
} 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>"

// Tool references
meta["tool_citations"] = ""
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