Swap sentieon/tnhaplotypecaller2 and tnscope to nf-test

modules/nf-core/sentieon/tnhaplotyper2/main.nf

@@ -21,9 +21,9 @@ process SENTIEON_TNHAPLOTYPER2 {
     val(emit_contamination_data)
 
     output:
-    tuple val(meta), path("*.orientation_data.tsv")  , optional:true , emit: orientation_data
-    tuple val(meta), path("*.contamination_data.tsv"), optional:true , emit: contamination_data
-    tuple val(meta), path("*.segments")              , optional:true , emit: contamination_segments
+    tuple val(meta), path("*.orientation_data.tsv")  , emit: orientation_data      , optional:true
+    tuple val(meta), path("*.contamination_data.tsv"), emit: contamination_data    , optional:true
+    tuple val(meta), path("*.segments")              , emit: contamination_segments, optional:true
     tuple val(meta), path("*.stats")                 , emit: stats
     tuple val(meta), path("*.vcf.gz")                , emit: vcf
     tuple val(meta), path("*.vcf.gz.tbi")            , emit: index
@@ -80,13 +80,16 @@ process SENTIEON_TNHAPLOTYPER2 {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix        = task.ext.prefix ?: "${meta.id}"
+    def orientation   = emit_orientation_data   ? "touch ${prefix}.orientation_data.tsv"              : ""
+    def contamination = emit_contamination_data ? "touch ${prefix}.{contamination_data.tsv,segments}" : ""
+
     """
-    touch ${prefix}.vcf.gz
+    echo | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
-    touch ${prefix}.contamination_data.tsv
-    touch ${prefix}.orientation_data.tsv
-    touch ${prefix}.segments
+    touch ${prefix}.vcf.gz.stats
+    $orientation
+    $contamination
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/sentieon/tnhaplotyper2/meta.yml

@@ -19,14 +19,14 @@ input:
         type: map
         description: |
           Groovy Map containing sample information.
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - input:
         type: file
-        description: BAM/CRAM file from alignment
+        description: BAM/CRAM file(s) from alignment
         pattern: "*.{bam,cram}"
     - input_index:
         type: file
-        description: BAI/CRAI file from alignment
+        description: BAI/CRAI file(s) from alignment
         pattern: "*.{bai,crai}"
     - intervals:
         type: file

modules/nf-core/sentieon/tnhaplotyper2/tests/main.nf.test

@@ -0,0 +1,293 @@
+nextflow_process {
+
+    name "Test Process SENTIEON_TNHAPLOTYPER2"
+    config "./nextflow.config"
+    script "../main.nf"
+    process "SENTIEON_TNHAPLOTYPER2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/addorreplacereadgroups"
+    tag "sentieon"
+    tag "sentieon/tnhaplotyper2"
+    config './nextflow.config'
+
+    setup {
+        run("PICARD_ADDORREPLACEREADGROUPS", alias: "NORMAL_ADDORREPLACEREADGROUPS") {
+            script "../../../picard/addorreplacereadgroups/main.nf"
+            config './nextflow.config'
+            process {
+                """
+                input[0] = [[id:'test'],
+                    [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists:true)]
+                    ]
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+
+        run("PICARD_ADDORREPLACEREADGROUPS", alias: "TUMOUR_ADDORREPLACEREADGROUPS") {
+            script "../../../picard/addorreplacereadgroups/main.nf"
+            config './nextflow.config'
+
+            process {
+                """
+                input[0] = [[id:'test'],
+                    [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists:true)]
+                    ]
+                input[1] = [[],[]]
+                input[2] = [[],[]]
+                """
+            }
+        }
+    }
+
+    test("tumour normal") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join( NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join( TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join( TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists:true)]
+                input[4] = [[:],[]]
+                input[5] = [[:],[]]
+                input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.summary,
+                    file(process.out.index[0][1]).name,
+                    process.out.stats,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+    }
+
+    test("tumour normal, with dbsnp and PoN") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', 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[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.summary,
+                    file(process.out.index[0][1]).name,
+                    process.out.stats,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+    }
+
+    test("tumour normal, with dbsnp and PoN, emit additional files") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = '--tumor_sample tumour'
+                module_args4 = '--tumor_sample tumour --normal_sample normal'
+            }
+            process {
+                """
+                input[0] = NORMAL_ADDORREPLACEREADGROUPS.out.bam
+                    .join(NORMAL_ADDORREPLACEREADGROUPS.out.bai)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bam)
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,normal_bam,normal_bai,tumour_bam,tumour_bai->
+                    [[id:'test'],[normal_bam,tumour_bam],[normal_bai,tumour_bai],[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', 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[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.summary,
+                    file(process.out.index[0][1]).name,
+                    process.out.stats,
+                    process.out.orientation_data,
+                    process.out.contamination_data,
+                    process.out.contamination_segments,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+    }
+
+    test("tumour only") {
+
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour'
+                module_args3 = '--tumor_sample tumour'
+                module_args4 = '--tumor_sample tumour'
+            }
+            process {
+                """
+                input[0] = TUMOUR_ADDORREPLACEREADGROUPS.out.bam
+                    .join(TUMOUR_ADDORREPLACEREADGROUPS.out.bai)
+                    .map{
+                    meta,tumour_bam,tumour_bai->
+                    [meta,tumour_bam,tumour_bai,[]]
+                    }
+                input[1] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists:true)]
+                input[2] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists:true)]
+                input[3] = [[:],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', 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[8] = true
+                input[9] = true
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    path(process.out.vcf[0][1]).vcf.summary,
+                    file(process.out.index[0][1]).name,
+                    process.out.versions,
+                    process.out.stats,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+    }
+
+
+    test("tumour normal - stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = [[id:'test'],[],[],[]]
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                input[5] = [[:],[]]
+                input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("tumour normal, emit additional files -stub") {
+        options '-stub'
+        when {
+            params {
+                module_args  = ''
+                module_args2 = '--tumor_sample tumour --normal_sample normal'
+                module_args3 = ''
+                module_args4 = ''
+            }
+            process {
+                """
+                input[0] = [[id:'test'],[],[],[]]
+                input[1] = [[:],[]]
+                input[2] = [[:],[]]
+                input[3] = [[:],[]]
+                input[4] = [[:],[]]
+                input[5] = [[:],[]]
+                input[6] = [[:],[]]
+                input[7] = [[:],[]]
+                input[8] = false
+                input[9] = false
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}