12801 bug in gsea module related with multiple gene sets processing

modules/nf-core/gsea/gsea/main.nf

@@ -43,28 +43,34 @@ process GSEA_GSEA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def rpt_label = prefix.replaceAll('\\.$', '') // Remove any trailing dots from prefix when passed as report label, so GSEA doesn't produce double-dotted top-level outputs
-    def chip_command = chip ? "-chip $chip -collapse true" : ''
+    def rpt_label = prefix.replaceAll('\\.$', '')
+    def chip_command = chip ? "-chip \"$chip\" -collapse true" : ''
+    // gsea-cli takes a comma-delimited -gmx value to pool multiple gene set files into one run.
+    def gmx = gene_sets instanceof List ? gene_sets.join(',') : gene_sets
 
     """
     # Run GSEA
 
     gsea-cli GSEA \\
-        -res $gct \\
-        -cls ${cls}#${target}_versus_${reference} \\
-        -gmx $gene_sets \\
+        -res "$gct" \\
+        -cls "${cls}#${target}_versus_${reference}" \\
+        -gmx "$gmx" \\
         $chip_command \\
         -out . \\
-        --rpt_label $rpt_label \\
+        --rpt_label "$rpt_label" \\
         $args
 
     # Un-timestamp the outputs for path consistency
-    mv ${rpt_label}.Gsea.*/* .
+    # Only rmdir actual directories: the .rpt file's name also matches "${rpt_label}.Gsea.*".
+    mv "$rpt_label".Gsea.*/* .
+    for gsea_dir in "$rpt_label".Gsea.*/; do
+        [ -d "\$gsea_dir" ] && rmdir "\$gsea_dir"
+    done
     timestamp=\$(cat *.rpt | grep producer_timestamp | awk '{print \$2}')
 
     for pattern in _\${timestamp} .\${timestamp}; do
         find . -name "*\${pattern}*" | sed "s|^\\./||" | while read -r f; do
-            mv \$f \${f//\$pattern/}
+            mv "\$f" "\${f//\$pattern/}"
         done
     done
     sed -i.bak "s/[_\\.]\$timestamp//g" *.rpt *.html && rm *.bak

modules/nf-core/gsea/gsea/tests/main.nf.test

@@ -59,6 +59,55 @@ nextflow_process {
         }
     }
 
+    test("test_multiple_gmt") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [['id':'Condition_genotype_WT_KO', 'variable':'Condition genotype', 'reference':'WT', 'target':'KO', 'blocking':'batch'], file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/Condition_treatment_Control_Treated.gct", checkIfExists:true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/Condition_genotype_WT_KO.cls", checkIfExists:true), [file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/mh.all.v2022.1.Mm.symbols.gmt", checkIfExists:true), file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/m5.mpt.v2022.1.Mm.symbols.gmt", checkIfExists:true)]]
+                input[1] = ['WT', 'KO']
+                input[2] = [
+                    ['id': 'test'],
+                    file("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/mus_musculus/gene_set_analysis/Mus_musculus.anno.feature_metadata.chip", checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.rpt.collect{ meta,rpt -> file(rpt).name }, //assert unstable file
+                    process.out.index_html.collect{ meta,index_html -> file(index_html).name }, //assert unstable file
+                    process.out.heat_map_corr_plot,
+                    process.out.report_tsvs_ref,
+                    process.out.report_htmls_ref.collect{ meta,report_htmls_ref -> file(report_htmls_ref).name }, //assert unstable file
+                    process.out.report_tsvs_target,
+                    process.out.report_htmls_target.collect{ meta,report_htmls_target -> file(report_htmls_target).name }, //assert unstable file
+                    process.out.ranked_gene_list,
+                    process.out.gene_set_sizes,
+                    process.out.histogram.collect{ meta,histogram -> file(histogram).name }, //assert unstable file
+                    process.out.heatmap.collect{ meta,heatmap -> file(heatmap).name }, //assert unstable file
+                    process.out.pvalues_vs_nes_plot.collect{ meta,pvalues_vs_nes_plot -> file(pvalues_vs_nes_plot).name }, //assert unstable file
+                    process.out.ranked_list_corr.collect{ meta,ranked_list_corr -> file(ranked_list_corr).name }, //assert unstable file
+                    process.out.butterfly_plot.collect{ meta,butterfly_plot -> file(butterfly_plot).name }, //assert unstable file
+                    process.out.gene_set_tsv,
+                    process.out.gene_set_html[0][1].collect{ file(it).name }, //assert unstable file
+                    process.out.gene_set_heatmap[0][1].collect{ file(it).name }, // unstable file and unstable name
+                    process.out.snapshot[0][1].collect{ file(it).name }, //assert unstable file
+                    process.out.gene_set_enplot[0][1].collect{ file(it).name }, // unstable file and unstable name
+                    process.out.gene_set_dist[0][1].collect{ file(it).name }, //assert unstable file
+                    process.out.archive,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    ).match()
+                }
+            )
+        }
+    }
+
     test("stub") {
 
         options "-stub"