From bf98197b0b3baf4c0e96e31fda48393c0688d112 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 6 May 2024 10:22:58 +0200
Subject: [PATCH] feat(subworkflow): update utils_nfcore_pipeline

---
 CHANGELOG.md                                       | 1 +
 modules.json                                       | 2 +-
 subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 +++++++-
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ed466343..a4ad42ad 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#74](https://github.com/nf-core/bamtofastq/pull/74) Update to samtools to v1.19.2
 - [#76](https://github.com/nf-core/bamtofastq/pull/76) Update modules cat/fastq and samtools/view
+- [#88](https://github.com/nf-core/bamtofastq/pull/88) Update subworkflow utils_nfcore_pipeline
 
 ### `Fixed`
 
diff --git a/modules.json b/modules.json
index b40e9d0c..e3d9f051 100644
--- a/modules.json
+++ b/modules.json
@@ -71,7 +71,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // 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
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +