From b63087e4bf960a032b67b0a9d382f69a451c4f3f Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 2 May 2024 11:52:44 +0200
Subject: [PATCH 1/4] fix(template): fix handling of multiple DOIs in manifest

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf       | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index e02a113755..07cbb0bc56 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -243,8 +243,14 @@ 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["nodoi_text"] = "<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"] = ""

From 13e5170296524e03f7b21543841b29848fc1e600 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <maxime.garcia@seqera.io>
Date: Thu, 2 May 2024 12:04:46 +0200
Subject: [PATCH 2/4] Update
 nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf             | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 07cbb0bc56..479900d5a9 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
@@ -248,9 +248,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
         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["nodoi_text"] = "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
-    }
+    } 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"] = ""

From f382f980a1be496e96726a8293ae9c031247f925 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 2 May 2024 18:23:42 +0200
Subject: [PATCH 3/4] handles doi.org resolver + comments

---
 .../local/utils_nfcore_pipeline_pipeline/main.nf         | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
index 479900d5a9..a4bfb9f8be 100644
--- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
+++ b/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>"
 

From fa0b60d642b964d7a32249d0838f6d39a0b8d9af Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 2 May 2024 18:24:41 +0200
Subject: [PATCH 4/4] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f0cca60b0d..d2a2bcf042 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 - Remove `pyproject.toml` from template root
 - Shorten lines in pipeline template ([#2908](https://github.com/nf-core/tools/pull/2908))
 - Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention ([#2936](https://github.com/nf-core/tools/pull/2936))
+- Handles multiple DOIs + doi.org resolver from manifest.doi ([#2946](https://github.com/nf-core/tools/pull/2946))
 
 ### Linting