Use original QC values for Deepvariant after BQSR

CHANGELOG.md

@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json
 - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
 - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
+- [1733](https://github.com/nf-core/sarek/pull/1733) - Use original quality values if DeepVariant is run on recalibrated data
 
 ### Removed
 

conf/modules/deepvariant.config

@@ -16,7 +16,10 @@
 process {
 
     withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
-        ext.args   = { params.wes ?  "--model_type=WES" : "--model_type=WGS" }
+        ext.args   = [
+            params.wes ?  "--model_type=WES" : "--model_type=WGS" ,
+            !params.skip_tools?.contains("baserecalibrator") ? "--make_examples_extra_args '--parse_sam_aux_fields=true,--use_original_quality_scores=true'" : ''
+        ].join(' ').trim()
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('deepvariant') }
         publishDir = [

nextflow.config

@@ -296,7 +296,6 @@ profiles {
     targeted                   { includeConfig 'conf/test/targeted.config' }
     tools                      { includeConfig 'conf/test/tools.config' }
     tools_germline             { includeConfig 'conf/test/tools_germline.config' }
-    tools_germline_deepvariant { includeConfig 'conf/test/tools_germline_deepvariant.config' }
     tools_somatic              { includeConfig 'conf/test/tools_somatic.config' }
     tools_somatic_ascat        { includeConfig 'conf/test/tools_somatic_ascat.config' }
     tools_tumoronly            { includeConfig 'conf/test/tools_tumoronly.config' }

tests/variant_calling_deepvariant.nf.test

@@ -0,0 +1,93 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --tools deepvariant") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                fasta     = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta"
+                fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta.fai"
+                intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.bed"
+                input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
+                outdir = "$outputDir"
+                nucleotides_per_second = 20
+                step = "variant_calling"
+                tools = 'deepvariant'
+                wes   = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools deepvariant --no_intervals") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                fasta     = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta"
+                fasta_fai = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta.fai"
+                intervals = "${params.modules_testdata_base_path}/genomics/homo_sapiens/genome/genome.bed"
+                input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv"
+                outdir = "$outputDir"
+                no_intervals = true
+                step = "variant_calling"
+                tools = 'deepvariant'
+                wes   = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+}