Fix: Cloud Storage objects are immutable on GCP

CHANGELOG.md

@@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#1378](https://github.com/nf-core/sarek/pull/1378) - Improve cloud tests launch workflow to use matrix
 - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline`
+- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491)
+- [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix multiple DOI handling in manifest
 
 ### Removed
 

nextflow.config

@@ -391,7 +391,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
     version         = '3.5.0dev'
-    doi             = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
+    doi             = '10.12688/f1000research.16665.2,10.1093/nargab/lqae031,10.5281/zenodo.3476425'
 }
 
 // Load modules.config for DSL2 module specific options

subworkflows/local/utils_nfcore_sarek_pipeline/main.nf

@@ -280,8 +280,14 @@ 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"] = ""

workflows/sarek/main.nf

@@ -879,7 +879,7 @@ workflow SAREK {
         ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files                      = ch_multiqc_files.mix(version_yaml)
         ch_multiqc_files                      = ch_multiqc_files.mix(reports)
-        ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+        ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))
 
         MULTIQC (
             ch_multiqc_files.collect(),