Add option to specify call for manta

CHANGELOG.md

@@ -8,11 +8,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows
+- Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers
 
 ### `Fixed`
 
 - Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#855](https://github.com/nf-core/raredisease/pull/855)
 
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+|               | cadd_prescored         |
+|               | manta_call_regions     |
+|               | manta_call_regions_tbi |
+
 ## 3.0.0 - Mario [2026-05-12]
 
 ### `Added`

docs/usage.md

@@ -263,10 +263,14 @@ The mandatory and optional parameters for each category are tabulated below.
 
 ##### 5. Variant calling - Structural variants
 
-| Mandatory | Optional   |
-| --------- | ---------- |
-|           | target_bed |
-|           | bwa        |
+| Mandatory | Optional                           |
+| --------- | ---------------------------------- |
+|           | target_bed                         |
+|           | bwa                                |
+|           | manta_call_regions<sup>1</sup>     |
+|           | manta_call_regions_tbi<sup>1</sup> |
+
+<sup>1</sup> A bgzipped BED file (`.bed.gz`) and its tabix index (`.bed.gz.tbi`) restricting Manta's SV calling to specific regions. Both parameters must be supplied together. Only applied for WGS; for WES, Manta always uses `target_bed` and these parameters have no effect. Useful for reducing runtime on references with many short contigs such as GRCh38 by limiting analysis to primary chromosomes.
 
 ##### 6. Copy number variant calling
 

main.nf

@@ -74,6 +74,8 @@ workflow NFCORE_RAREDISEASE {
     val_known_dbsnp_tbi
     val_light_strand_origin_end
     val_light_strand_origin_start
+    val_manta_call_regions
+    val_manta_call_regions_tbi
     val_mbuffer_mem
     val_mito_length
     val_mito_name
@@ -262,6 +264,11 @@ workflow NFCORE_RAREDISEASE {
 
     ch_cadd_header              = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect()
     ch_foundin_header           = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect()
+    ch_manta_regions            = val_analysis_type.equals("wgs")
+                                    ? (val_manta_call_regions
+                                        ? channel.value([file(val_manta_call_regions), file(val_manta_call_regions_tbi)])
+                                        : channel.value([[], []]))
+                                    : ch_target_bed.map { _meta, bed, tbi -> [bed, tbi] }
     ch_ngsbits_method           = channel.value(val_ngsbits_samplegender_method)
     ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model)
     ch_subdepth                 = channel.value(val_subdepth)
@@ -404,6 +411,7 @@ workflow NFCORE_RAREDISEASE {
         ch_hgnc_ids,
         ch_intervals_wgs,
         ch_intervals_y,
+        ch_manta_regions,
         ch_me_references,
         ch_me_svdb_resources,
         ch_ml_model,
@@ -595,6 +603,8 @@ workflow {
         params.known_dbsnp_tbi,
         params.light_strand_origin_end,
         params.light_strand_origin_start,
+        params.manta_call_regions,
+        params.manta_call_regions_tbi,
         params.mbuffer_mem,
         params.mito_length,
         params.mito_name,

nextflow.config

@@ -55,6 +55,8 @@ params {
     call_interval                   = null
     cadd_prescored                  = null
     cadd_resources                  = null
+    manta_call_regions              = null
+    manta_call_regions_tbi          = null
     gcnvcaller_model                = null
     gens_interval_list              = null
     gens_pon_female                 = null

nextflow_schema.json

@@ -243,6 +243,23 @@
                     "description": "Local directory base for genome references that map to the config.",
                     "help_text": "This folder is a flat structure with file names that map to the config."
                 },
+                "manta_call_regions": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "file-path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\.bed\\.gz$",
+                    "description": "Path to a bgzipped BED file restricting Manta SV calling to specific regions (e.g. primary chromosomes). Only applied for WGS; for WES, Manta always uses target_bed instead.",
+                    "help_text": "Must be supplied together with --manta_call_regions_tbi. Only used when analysis_type is wgs — for wes, Manta uses the target_bed supplied via --target_bed and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38."
+                },
+                "manta_call_regions_tbi": {
+                    "type": "string",
+                    "exists": true,
+                    "format": "file-path",
+                    "fa_icon": "fas fa-file",
+                    "pattern": "^\\S+\\.bed\\.gz\\.tbi$",
+                    "description": "Tabix index for the file supplied via --manta_call_regions."
+                },
                 "mito_name": {
                     "type": "string",
                     "description": "Name of the mitochondrial contig in the reference fasta file",

subworkflows/local/call_structural_variants/main.nf

@@ -24,6 +24,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
         ch_genome_fai                         // channel: [mandatory] [ val(meta), path(fai) ]
         ch_genome_fasta                       // channel: [mandatory] [ val(meta), path(fasta) ]
         ch_genome_hisat2index                 // channel: [mandatory] [ val(meta), path(hisat2index) ]
+        ch_manta_regions                      // channel: [mandatory] [ path(bed), path(tbi) ]
         ch_mitosalt_config                    // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)]
         ch_mt_bam_bai                         // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
         ch_mt_fai                             // channel: [mandatory] [ val(meta), path(mtfai) ]
@@ -34,7 +35,6 @@ workflow CALL_STRUCTURAL_VARIANTS {
         ch_reads                              // channel: [mandatory] [ val(meta), [path(reads)] ]
         ch_subdepth                           // channel: [mandatory] [ val(mitosalt_depth) ]
         ch_svcaller_priority                  // channel: [mandatory] [ val(["var caller tag 1", ...]) ]
-        ch_target_bed                         // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ]
         skip_germlinecnvcaller                // boolean
         skip_mitosalt                         // boolean
         val_analysis_type                     // string: "wes", "wgs", or "mito"
@@ -59,7 +59,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
         ch_tiddit_vcf     = channel.empty()
 
         if (!val_analysis_type.equals("mito")) {
-            CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type)
+            CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_manta_regions)
                 .filtered_diploid_sv_vcf
                 .collect{ _meta, vcf -> vcf }
                 .set{ ch_manta_vcf }

subworkflows/local/call_structural_variants/tests/main.nf.test

@@ -42,27 +42,27 @@ nextflow_workflow {
                 input[8]  = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect()
                 input[9]  = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect()
                 input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] }
-                input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15])
-                input[12] = channel.of([
+                input[11] = channel.value([[], []])
+                input[12] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15])
+                input[13] = channel.of([
                     [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
                     file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true),
                     file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)
                 ])
-                input[13] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect()
-                input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect()
-                input[15] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] }
-                input[16] = channel.of([[id:'ploidy'], []])
-                input[17] = channel.of([[]])
-                input[18] = channel.of([
+                input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect()
+                input[15] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect()
+                input[16] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] }
+                input[17] = channel.of([[id:'ploidy'], []])
+                input[18] = channel.of([[]])
+                input[19] = channel.of([
                     [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'],
                     [
                         file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true),
                         file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)
                     ]
                 ])
-                input[19] = channel.value(10000000)
-                input[20] = channel.value(['manta', 'tiddit', 'cnvnator'])
-                input[21] = channel.of([[id:'target'], [], []])
+                input[20] = channel.value(10000000)
+                input[21] = channel.value(['manta', 'tiddit', 'cnvnator'])
                 input[22] = true
                 input[23] = false
                 input[24] = 'wgs'

subworkflows/local/call_structural_variants/tests/main.nf.test.snap

@@ -16,10 +16,10 @@
                 "justhusky_sv.vcf.gz.tbi"
             ]
         ],
+        "timestamp": "2026-04-14T15:51:47.077800376",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-04-14T15:51:47.077800376"
+        }
     }
 }

subworkflows/local/call_sv_manta/main.nf

@@ -7,13 +7,12 @@ include { MANTA_GERMLINE as MANTA              } from '../../../modules/nf-core/
 
 workflow CALL_SV_MANTA {
     take:
-        ch_bam            // channel: [mandatory] [ val(meta), path(bam) ]
-        ch_bai            // channel: [mandatory] [ val(meta), path(bai) ]
-        ch_genome_fasta   // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_genome_fai     // channel: [mandatory] [ val(meta), path(fai) ]
-        ch_case_info      // channel: [mandatory] [ val(case_info) ]
-        ch_bed            // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ]
-        val_analysis_type // string: "wes", "wgs", or "mito"
+        ch_bam          // channel: [mandatory] [ val(meta), path(bam) ]
+        ch_bai          // channel: [mandatory] [ val(meta), path(bai) ]
+        ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_genome_fai   // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_case_info    // channel: [mandatory] [ val(case_info) ]
+        ch_regions      // channel: [mandatory] [ path(bed), path(tbi) ]
 
     main:
         ch_bam.map{ _meta, bam -> bam }
@@ -26,24 +25,11 @@ workflow CALL_SV_MANTA {
             .toList()
             .set { bai_file_list }
 
-        ch_bed.map {
-                _id, bed_file, index ->
-                    return [bed_file, index]}
-            .set { bed_input }
-
-        if (val_analysis_type.equals("wgs")) {
-            ch_case_info.combine(bam_file_list)
-                .combine(bai_file_list)
-                .map { meta, input, index -> [meta, input, index] + [ [], [] ] }
-                .set { manta_input }
-            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
-        } else {
-            ch_case_info.combine(bam_file_list)
-                .combine(bai_file_list)
-                .combine(bed_input)
-                .set { manta_input }
-            MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
-        }
+        ch_case_info.combine(bam_file_list)
+            .combine(bai_file_list)
+            .combine(ch_regions)
+            .set { manta_input }
+        MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
 
         MANTA.out.diploid_sv_vcf
             .join(MANTA.out.diploid_sv_vcf_tbi)

subworkflows/local/call_sv_manta/tests/main.nf.test

@@ -12,7 +12,7 @@ nextflow_workflow {
 
     config "./nextflow.config"
 
-    test("CALL_SV_MANTA - wgs") {
+    test("CALL_SV_MANTA") {
 
         when {
             workflow {
@@ -36,8 +36,7 @@ nextflow_workflow {
                 input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
                 input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4] = channel.of([id:'justhusky'])
-                input[5] = channel.of([[id:'target'], [], []])
-                input[6] = 'wgs'
+                input[5] = channel.value([[], []])
                 """
             }
         }
@@ -52,7 +51,7 @@ nextflow_workflow {
             )
         }
     }
-    test("CALL_SV_MANTA - wgs, stub") {
+    test("CALL_SV_MANTA - stub") {
 
         options "-stub"
 
@@ -78,8 +77,7 @@ nextflow_workflow {
                 input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect()
                 input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect()
                 input[4] = channel.of([id:'justhusky'])
-                input[5] = channel.of([[id:'target'], [], []])
-                input[6] = 'wgs'
+                input[5] = channel.value([[], []])
                 """
             }
         }

subworkflows/local/call_sv_manta/tests/main.nf.test.snap

@@ -1,16 +1,16 @@
 {
-    "CALL_SV_MANTA - wgs": {
+    "CALL_SV_MANTA": {
         "content": [
             "9f37331609347a1685ba4862d8583b2f",
             "2111e88e54fdd01f0492901606bcea6f"
         ],
-        "timestamp": "2026-03-01T20:55:33.556714847",
+        "timestamp": "2026-06-03T11:38:41.791162924",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.5",
             "nextflow": "25.10.4"
         }
     },
-    "CALL_SV_MANTA - wgs, stub": {
+    "CALL_SV_MANTA - stub": {
         "content": [
             {
                 "0": [
@@ -127,9 +127,9 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-05T12:58:54.578278212",
+        "timestamp": "2026-06-03T11:39:05.440330127",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.5",
             "nextflow": "25.10.4"
         }
     }

workflows/raredisease.nf

@@ -104,6 +104,7 @@ workflow RAREDISEASE {
     ch_hgnc_ids
     ch_intervals_wgs
     ch_intervals_y
+    ch_manta_regions
     ch_me_references
     ch_me_svdb_resources
     ch_ml_model
@@ -636,6 +637,7 @@ workflow RAREDISEASE {
             ch_genome_fai,
             ch_genome_fasta,
             ch_genome_hisat2index,
+            ch_manta_regions,
             ch_mitosalt_config,
             ch_mapped.mt_bam_bai,
             ch_mt_fai,
@@ -646,7 +648,6 @@ workflow RAREDISEASE {
             ch_input_fastqs,
             ch_subdepth,
             ch_svcaller_priority,
-            ch_target_bed,
             skip_germlinecnvcaller,
             skip_mitosalt,
             val_analysis_type,