From 36ad41b0e4a6619a0f6b594880db9b769a9b4c83 Mon Sep 17 00:00:00 2001
From: nicorap <78540495+nicorap@users.noreply.github.com>
Date: Mon, 11 May 2026 12:00:10 +0200
Subject: [PATCH 1/2] fix: sentieon gvcftyper accepts intervals

---
 modules/nf-core/sentieon/gvcftyper/main.nf    |  3 +-
 .../sentieon/gvcftyper/tests/main.nf.test     | 39 +++++++++++++++++++
 2 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
index af3cbdcf689c..b002b20c7775 100644
--- a/modules/nf-core/sentieon/gvcftyper/main.nf
+++ b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -27,13 +27,14 @@ process SENTIEON_GVCFTYPER {
     def prefix = task.ext.prefix ?: "${meta.id}_genotyped"
     def gvcfs_input = '-v ' + gvcfs.join(' -v ')
     def dbsnp_cmd = dbsnp ? "--dbsnp ${dbsnp}" : ""
+    def interval_command = intervals ? "--interval ${intervals}" : ""
     def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64
         ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; "
         : ""
     """
     ${sentieonLicense}
 
-    sentieon driver -r ${fasta} --algo GVCFtyper ${gvcfs_input} ${dbsnp_cmd} ${prefix}.vcf.gz
+    sentieon driver -r ${fasta} ${interval_command} --algo GVCFtyper ${gvcfs_input} ${dbsnp_cmd} ${prefix}.vcf.gz
 
     """
 
diff --git a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test
index a32a8d85eddd..5c810f438817 100644
--- a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test
+++ b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test
@@ -170,6 +170,45 @@ nextflow_process {
         }
     }
 
+    test("sentieon gvcftyper intervals constrain output - regression") {
+        // Regression test for the bug where `path(intervals)` was staged but
+        // never passed to `sentieon driver --interval`, causing GVCFtyper to
+        // run unconstrained. Before the fix, the variantsMD5 of an intervals
+        // run was identical to the no-intervals run
+        // ("d13216836f1452e200b215b796606671"). After the fix, the bed must
+        // actually restrict GVCFtyper, so the md5 MUST differ.
+
+        when {
+            process {
+                """
+                input[0] =  [ [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics//homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                            ]
+
+                input[1] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]
+                input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]
+                input[3] = [[:], []]
+                input[4] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert path(process.out.vcf_gz[0][1]).vcf.variantsMD5 != "d13216836f1452e200b215b796606671" },
+                { assert snapshot(
+                        process.out.findAll { key, val -> key.startsWith("versions") },
+                        file(process.out.vcf_gz_tbi.get(0).get(1)).name,
+                        path(process.out.vcf_gz[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+    }
+
     test("sentieon gvcftyper - stub") {
 
         options "-stub"

From c3656d80bd7b32075c5b78f684ecde5f31663a96 Mon Sep 17 00:00:00 2001
From: nicorap <78540495+nicorap@users.noreply.github.com>
Date: Fri, 15 May 2026 09:17:37 +0200
Subject: [PATCH 2/2] style: line breaks in sentieon gvcftyper driver call
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

  Per @SPPearce review on #11582 — match the multi-line format used
  in sentieon/haplotyper.
---
 modules/nf-core/sentieon/gvcftyper/main.nf | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
index b002b20c7775..9ef05cbcaaa0 100644
--- a/modules/nf-core/sentieon/gvcftyper/main.nf
+++ b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -34,7 +34,13 @@ process SENTIEON_GVCFTYPER {
     """
     ${sentieonLicense}
 
-    sentieon driver -r ${fasta} ${interval_command} --algo GVCFtyper ${gvcfs_input} ${dbsnp_cmd} ${prefix}.vcf.gz
+    sentieon driver \\
+        -r ${fasta} \\
+        ${interval_command} \\
+        --algo GVCFtyper \\
+        ${gvcfs_input} \\
+        ${dbsnp_cmd} \\
+        ${prefix}.vcf.gz
 
     """