Port pytest to nftest for sentieon/haplotyper (#6069)

* Port pytest to nftest for sentieon/haplotyper * fix stub tests * ditch conda
nf-core · Jul 31, 2024 · 409e81a · 409e81a
1 parent e5ac715
commit 409e81a
Show file tree

Hide file tree

Showing 10 changed files with 406 additions and 167 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -606,6 +606,8 @@ jobs:
             path: modules/nf-core/sentieon/bwamem
           - profile: conda
             path: modules/nf-core/sentieon/dedup
+          - profile: conda
+            path: modules/nf-core/sentieon/haplotyper
           - profile: conda
             path: modules/nf-core/sentieon/qualcal
           - profile: conda

diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf
@@ -10,10 +10,10 @@ process SENTIEON_HAPLOTYPER {
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
-    path  fasta
-    path  fai
-    path  dbsnp
-    path  dbsnp_tbi
+    tuple val(meta1), path(fasta)
+    tuple val(meta2), path(fai)
+    tuple val(meta3), path(dbsnp)
+    tuple val(meta4), path(dbsnp_tbi)
     val(emit_vcf)
     val(emit_gvcf)
 
@@ -63,9 +63,9 @@ process SENTIEON_HAPLOTYPER {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.unfiltered.vcf.gz
+    echo "" | gzip > ${prefix}.unfiltered.vcf.gz
     touch ${prefix}.unfiltered.vcf.gz.tbi
-    touch ${prefix}.g.vcf.gz
+    echo "" | gzip > ${prefix}.g.vcf.gz
     touch ${prefix}.g.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test
@@ -0,0 +1,220 @@
+nextflow_process {
+
+    name "Test Process SENTIEON_HAPLOTYPER"
+    script "../main.nf"
+    process "SENTIEON_HAPLOTYPER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sentieon"
+    tag "sentieon/haplotyper"
+
+    test("Sentieon Haplotyper VCF") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                           []  // no intervals
+                        ]
+                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] = [[:],[]]
+                input[5] = 'variant'
+                input[6] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.versions,
+                        file(process.out.vcf_tbi.get(0).get(1)).name,
+                        path(process.out.vcf[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("Sentieon Haplotyper GVCF") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                           []  // no intervals
+                        ]
+                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] = [[:],[]]
+                input[5] = ''
+                input[6] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.versions,
+                        file(process.out.gvcf_tbi.get(0).get(1)).name,
+                        path(process.out.gvcf[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("Sentieon Haplotyper BOTH") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                           []  // no intervals
+                        ]
+                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] = [[:],[]]
+                input[5] = 'variant'
+                input[6] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.versions,
+                        file(process.out.gvcf_tbi.get(0).get(1)).name,
+                        path(process.out.gvcf[0][1]).vcf.variantsMD5,
+                        file(process.out.vcf_tbi.get(0).get(1)).name,
+                        path(process.out.vcf[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("Sentieon Haplotyper Intervals BOTH") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', 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] = [[:],[]]
+                input[5] = 'variant'
+                input[6] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.versions,
+                        file(process.out.gvcf_tbi.get(0).get(1)).name,
+                        path(process.out.gvcf[0][1]).vcf.variantsMD5,
+                        file(process.out.vcf_tbi.get(0).get(1)).name,
+                        path(process.out.vcf[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("Sentieon Haplotyper DBSNP BOTH") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', 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] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]
+                input[4] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]
+                input[5] = 'variant'
+                input[6] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.versions,
+                        file(process.out.gvcf_tbi.get(0).get(1)).name,
+                        path(process.out.gvcf[0][1]).vcf.variantsMD5,
+                        file(process.out.vcf_tbi.get(0).get(1)).name,
+                        path(process.out.vcf[0][1]).vcf.variantsMD5
+                    ).match()
+                }
+            )
+        }
+    }
+
+
+    test("Sentieon Haplotyper - stub") {
+
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
+                           []  // no intervals
+                        ]
+                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] = [[:],[]]
+                input[5] = ''
+                input[6] = false
+                """
+            }
+        }
+
+        then {
+
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+
+        }
+    }
+
+}