Finding more issues

nf-core · Oct 11, 2024 · f7baad5 · f7baad5
1 parent cfe34d6
commit f7baad5
Showing 1 changed file with 0 additions and 21 deletions.
diff --git a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
@@ -57,8 +57,6 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    UTILS_NFSCHEMA_PLUGIN (
-        workflow,
     UTILS_NFSCHEMA_PLUGIN (
         workflow,
         validate_params,
@@ -97,9 +95,6 @@ workflow PIPELINE_INITIALISATION {
         .groupTuple()
         .map { samplesheet ->
             validateInputSamplesheet(samplesheet)
-        .map { samplesheet ->
-            validateInputSamplesheet(samplesheet)
-        }
         .map {
             meta, fastqs ->
                 return [ meta, fastqs.flatten() ]
@@ -148,15 +143,6 @@ workflow PIPELINE_COMPLETION {
                 monochrome_logs,
                 multiqc_report.toList()
             )
-            completionEmail(
-                summary_params,
-                email,
-                email_on_fail,
-                plaintext_email,
-                outdir,
-                monochrome_logs,
-                multiqc_report.toList()
-            )
         }
 
         completionSummary(monochrome_logs)
@@ -225,7 +211,6 @@ def validateInputSamplesheet(input) {
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
     def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
-    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
@@ -335,10 +320,6 @@ def methodsDescriptionText(mqc_methods_yaml) {
         manifest_doi.each { doi_ref ->
             temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
         }
-        def manifest_doi = meta.manifest_map.doi.tokenize(",")
-        manifest_doi.each { doi_ref ->
-            temp_doi_ref += "(doi: <a href=\'https://doi.org/${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>"
@@ -358,5 +339,3 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     return description_html.toString()
 }
-
-