Update gatk4 mutect2 to add --alleles parameter for force calling

modules/nf-core/gatk4/mutect2/main.nf

@@ -12,6 +12,8 @@ process GATK4_MUTECT2 {
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
     tuple val(meta4), path(dict)
+    path alleles
+    path alleles_tbi
     path germline_resource
     path germline_resource_tbi
     path panel_of_normals
@@ -34,6 +36,7 @@ process GATK4_MUTECT2 {
     def interval_command = intervals ? "--intervals ${intervals}" : ""
     def pon_command = panel_of_normals ? "--panel-of-normals ${panel_of_normals}" : ""
     def gr_command = germline_resource ? "--germline-resource ${germline_resource}" : ""
+    def a_command = alleles ? "--alleles ${alleles}": ""
 
     def avail_mem = 3072
     if (!task.memory) {
@@ -50,6 +53,7 @@ process GATK4_MUTECT2 {
         --reference ${fasta} \\
         ${pon_command} \\
         ${gr_command} \\
+        ${a_command} \\
         ${interval_command} \\
         --tmp-dir . \\
         ${args}

modules/nf-core/gatk4/mutect2/meta.yml

@@ -68,6 +68,17 @@ input:
         description: GATK sequence dictionary
         pattern: "*.dict"
         ontologies: []
+  - alleles:
+      type: file
+      description: vcf file to be used to force-call alleles.
+      pattern: "*.vcf.gz"
+      ontologies:
+        - edam: http://edamontology.org/format_3989 # GZIP format
+  - alleles_tbi:
+      type: file
+      description: Index file for alleles to be force-called.
+      pattern: "*.vcf.gz.tbi"
+      ontologies: []
   - germline_resource:
       type: file
       description: Population vcf of germline sequencing, containing allele fractions.
@@ -143,3 +154,4 @@ authors:
 maintainers:
   - "@GCJMackenzie"
   - "@ramprasadn"
+

modules/nf-core/gatk4/mutect2/tests/main.nf.test

@@ -45,10 +45,12 @@ nextflow_process {
                 [ id:'genome' ],
                 file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
             ]
-            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
-            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
-            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[4] = []
+            input[5] = []
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
             """
             }
         }
@@ -105,10 +107,12 @@ nextflow_process {
                 [ id:'genome' ],
                 file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
             ]
-            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
-            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
-            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[4] = []
+            input[5] = []
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
             """
             }
         }
@@ -127,6 +131,7 @@ nextflow_process {
             )
         }
     }
+
     test("human - bam - tumor_only"){
         when {
             params {
@@ -152,10 +157,12 @@ nextflow_process {
                 [ id:'genome' ],
                 file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
             ]
-            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
-            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
-            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[4] = []
+            input[5] = []
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
             """
             }
         }
@@ -174,6 +181,7 @@ nextflow_process {
             )
         }
     }
+
     test("human - cram"){
         when {
             params {
@@ -199,10 +207,12 @@ nextflow_process {
                 [ id:'genome' ],
                 file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
             ]
-            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
-            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
-            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[4] = []
+            input[5] = []
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
             """
             }
         }
@@ -251,6 +261,8 @@ nextflow_process {
             input[5] = []
             input[6] = []
             input[7] = []
+            input[8] = []
+            input[9] = []
             """
             }
         }
@@ -299,6 +311,8 @@ nextflow_process {
             input[5] = []
             input[6] = []
             input[7] = []
+            input[8] = []
+            input[9] = []
             """
             }
         }
@@ -356,10 +370,12 @@ nextflow_process {
                 [ id:'genome' ],
                 file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
             ]
-            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
-            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
-            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[4] = []
+            input[5] = []
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
             """
             }
         }
@@ -372,4 +388,115 @@ nextflow_process {
 
     }
 
+    test("human - bam - tumor_normal_pair - force_call") {
+        when {
+            params {
+                module_args = ""
+            }
+            process {
+            """
+            input[0] = [
+                [
+                    id:'test',
+                    normal_id:'normal',
+                    tumor_id:'tumour'
+                ],
+                [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true)
+                ],
+                [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ],
+                []
+            ]
+            input[1] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+            ]
+            input[2] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+            ]
+            input[3] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+            ]
+            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz', checkIfExists: true)
+            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                        process.out.tbi.collect { file(it[1]).getName() },
+                        process.out.stats,
+                        process.out.f1r2,
+                        process.out.versions,
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("human - bam - tumor_only - force_call"){
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+            """
+            input[0] = [
+                [ id:'test'],
+                [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true)],
+                [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)],
+                []
+            ]
+            input[1] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+            ]
+            input[2] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+            ]
+            input[3] = [
+                [ id:'genome' ],
+                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true)
+            ]
+            input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz', checkIfExists: true)
+            input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', checkIfExists: true)
+            input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true)
+            input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true)
+            input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+            input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+            """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                        process.out.tbi.collect { file(it[1]).getName() },
+                        process.out.stats,
+                        process.out.f1r2,
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
 }