Fix NETMHCSTABANDPAN to support samples without SV data

subworkflows/msk/netmhcstabandpan/main.nf

@@ -58,16 +58,19 @@ def createNETMHCInput(fastas_and_hla, sv_fastas) {
                 [it[0],it]
                 }
 
+        // remainder: true keeps samples that have no SV data (sv_fastas is empty when no SVs provided)
         def merged_mut = fastas_and_hla_channel
-            .join(sv_fastas_channel, by:0)
+            .join(sv_fastas_channel, by:0, remainder: true)
             .map({
-                [it[1][0], it[1][1], it[2][1], it[1][3], "MUT"]
+                def sv = it[2] ?: [null, [], []]
+                [it[1][0], it[1][1], sv[1], it[1][3], "MUT"]
             })
 
         def merged_wt = fastas_and_hla_channel
-            .join(sv_fastas_channel, by:0)
+            .join(sv_fastas_channel, by:0, remainder: true)
             .map({
-                [it[1][0], it[1][2], it[2][2], it[1][3], "WT"]
+                def sv = it[2] ?: [null, [], []]
+                [it[1][0], it[1][2], sv[2], it[1][3], "WT"]
             })
         def merged = merged_mut.mix(merged_wt)
         return merged

subworkflows/msk/netmhcstabandpan/tests/main.nf.test

@@ -162,6 +162,43 @@ nextflow_workflow {
     }
 
 
+    test("netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub") {
+
+        // Regression test: when no SV files are provided, the upstream NEOSV process
+        // doesn't run, so the sv_fasta channel emits zero items. The createNETMHCInput
+        // helper must still emit MUT and WT tuples for each sample.
+
+        options "-stub"
+
+        when {
+            workflow {
+                """
+                input[0] = channel.value([
+                    [ id:'test', single_end:false ], // meta map
+                    file('MUT_sequence_fa', checkIfExists: false),
+                    file('WT_sequence_fa', checkIfExists: false),
+                    "HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
+                    ])
+
+                input[1] = channel.empty()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out.tsv[0][0],
+                                  file(workflow.out.tsv[0][1]).name,
+                                  workflow.out.tsv[1][0],
+                                  file(workflow.out.tsv[1][1]).name
+                                  ).match()
+                }
+            )
+        }
+    }
+
+
     test("netmhcstabandpan - fa,hla_str - tsv - stub") {
 
         options "-stub"

subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap

@@ -212,5 +212,30 @@
             "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-19T14:22:41.854041255"
+    },
+    "netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub": {
+        "content": [
+            {
+                "id": "test",
+                "single_end": false,
+                "typeMut": false,
+                "fromStab": false,
+                "typePan": true
+            },
+            "test.WT.PAN.tsv",
+            {
+                "id": "test",
+                "single_end": false,
+                "typeMut": false,
+                "fromStab": true,
+                "typePan": true
+            },
+            "test.WT.STAB.tsv"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2026-05-13T22:29:19.315483"
     }
 }