Update strelka, by enabling BP if Manta candidates are present (#923)

* add BP to strelka/somatic

* merge conflicts

* update strelka modules for BP

* update strelka modules for BP

* apply suggestions from code review

modules/strelka/germline/main.nf

@@ -52,7 +52,7 @@ process STRELKA_GERMLINE {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( configureStrelkaSomaticWorkflow.py --version )
+        ${getSoftwareName(task.process)}: \$( configureStrelkaGermlineWorkflow.py --version )
     END_VERSIONS
     """
 }

modules/strelka/somatic/main.nf

@@ -19,7 +19,7 @@ process STRELKA_SOMATIC {
     }
 
     input:
-    tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor)
+    tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor),  path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
     path  fasta
     path  fai
     path  target_bed
@@ -34,13 +34,15 @@ process STRELKA_SOMATIC {
 
     script:
     def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def options_strelka = target_bed ? "--exome --callRegions ${target_bed}" : ""
+    def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : ""
+    def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : ""
     """
     configureStrelkaSomaticWorkflow.py \\
         --tumor $cram_tumor \\
         --normal $cram_normal \\
         --referenceFasta $fasta \\
-        $options_strelka \\
+        $options_target_bed \\
+        $options_manta \\
         $options.args \\
         --runDir strelka
 

modules/strelka/somatic/meta.yml

@@ -37,6 +37,14 @@ input:
       type: file
       description: BAM/CRAM/SAM index file
       pattern: "*.{bai,crai,sai}"
+  - manta_candidate_small_indels:
+      type: file
+      description: VCF.gz file
+      pattern: "*.{vcf.gz}"
+  - manta_candidate_small_indels_tbi:
+      type: file
+      description: VCF.gz index file
+      pattern: "*.tbi"
   - fasta:
       type: file
       description: Genome reference FASTA file

tests/modules/strelka/somatic/main.nf

@@ -11,7 +11,28 @@ workflow test_strelka_somatic {
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        [],[]
+    ]
+
+    fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bed     = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
+
+    STRELKA_SOMATIC (input, fasta, fai, bed, bed_tbi )
+}
+
+workflow test_strelka__best_practices_somatic {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
     ]
 
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)

tests/modules/strelka/somatic/test.yml

@@ -10,3 +10,16 @@
     - path: output/strelka/test.somatic_snvs.vcf.gz
     - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+
+- name: strelka somatic test_strelka__best_practices_somatic
+  command: nextflow run tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c tests/config/nextflow.config
+  tags:
+    - strelka
+    - strelka/somatic
+  files:
+    - path: output/strelka/test.somatic_indels.vcf.gz
+    - path: output/strelka/test.somatic_indels.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905
+    - path: output/strelka/test.somatic_snvs.vcf.gz
+    - path: output/strelka/test.somatic_snvs.vcf.gz.tbi
+      md5sum: 4cb176febbc8c26d717a6c6e67b9c905