Merge pull request #1725 from nvnieuwk/add-dragstrmodel-to-haplotypecaller

add dragstr model to haplotypecaller

modules/gatk4/haplotypecaller/main.nf

@@ -8,7 +8,7 @@ process GATK4_HAPLOTYPECALLER {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(intervals)
+    tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
     path  fasta
     path  fai
     path  dict
@@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
     def interval_command = intervals ? "--intervals $intervals" : ""
+    def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
         --reference $fasta \\
         $dbsnp_command \\
         $interval_command \\
+        $dragstr_command \\
         --tmp-dir . \\
         $args
 

modules/gatk4/haplotypecaller/meta.yml

@@ -32,6 +32,10 @@ input:
   - intervals:
       type: file
       description: Bed file with the genomic regions included in the library (optional)
+  - dragstr_model:
+      type: file
+      description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
+      pattern: "*.txt"
   - fasta:
       type: file
       description: The reference fasta file

tests/config/test_data.config

@@ -266,6 +266,8 @@ params {
                 test_pileups_table                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
                 test2_pileups_table                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
 
+                test_paired_end_sorted_dragstrmodel            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
+
                 test_genomicsdb_tar_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
                 test_pon_genomicsdb_tar_gz                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
 

tests/modules/gatk4/haplotypecaller/main.nf

@@ -8,6 +8,7 @@ workflow test_gatk4_haplotypecaller {
     input     = [ [ id:'test' ], // meta map
                   file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
                   file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                  [],
                   []
                 ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@@ -21,6 +22,7 @@ workflow test_gatk4_haplotypecaller_cram {
     input = [ [ id:'test' ], // meta map
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
                 []
               ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@@ -34,7 +36,8 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
    input = [ [ id:'test' ], // meta map
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+                []
             ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@@ -45,3 +48,20 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
 
     GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
 }
+
+workflow test_gatk4_haplotypecaller_dragstr_model {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], 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)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = []
+    sites_tbi = []
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
+}

tests/modules/gatk4/haplotypecaller/test.yml

@@ -6,7 +6,6 @@
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
   command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
@@ -16,7 +15,6 @@
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
   command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
@@ -26,4 +24,12 @@
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
+
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi