adding files for inputs and remove scripts

.dockstore.yml

@@ -139,3 +139,8 @@ workflows:
    primaryDescriptorPath: /CNV_Array_Prober/cnvArrayProber.wdl
    testParameterFiles:
     - /CNV_Array_Prober/cnvArrayProber.inputs.json
+ - name: CallabilityAnalysis
+   subclass: WDL
+   primaryDescriptorPath: /CallabilityAnalysis/CallabilityAnalysis.wdl
+   testParameterFiles:
+    - /CallabilityAnalysis/CallabilityAnalysis.inputs.json

CallabilityAnalysis/CallabilityAnalysis.inputs.json

@@ -0,0 +1 @@
+{"Callability_Analysis.ref_bwt":"${workspace.referenceData_hg38_ref_bwt}","Callability_Analysis.summarize_coverage.disk_size":"${16}","Callability_Analysis.ref_dict":"${workspace.referenceData_hg38_ref_dict}","Callability_Analysis.GenerateAnnotation.maxRetries":"${}","Callability_Analysis.exome_bed":"gs://gptag/AnnotateBed/bed_for_all_exon.hg38.bed","Callability_Analysis.chrX_name":"chrX","Callability_Analysis.sample_fraction":"${80}","Callability_Analysis.min_mapping_quality":"${20}","Callability_Analysis.interval_list":"gs://fc-8123e6b7-c245-489c-9a28-5ebbd128458d/redo_analysis/16bp_padded_nurture_CDS.hg38.interval_list","Callability_Analysis.ref_amb":"${workspace.referenceData_hg38_ref_amb}","Callability_Analysis.coverage_mem_gb":"${64}","Callability_Analysis.ref_index":"${workspace.referenceData_hg38_ref_fasta_index}","Callability_Analysis.gene_list":"${}","Callability_Analysis.GenerateAnnotation.diskGB":"${}","Callability_Analysis.chrY_name":"chrY","Callability_Analysis.ref_sa":"${workspace.referenceData_hg38_ref_sa}","Callability_Analysis.bam_or_cram_paths":"${this.samples.cram}","Callability_Analysis.ref_pac":"${workspace.referenceData_hg38_ref_pac}","Callability_Analysis.GenerateAnnotation.preemptible":"${}","Callability_Analysis.ref_ann":"${workspace.referenceData_hg38_ref_ann}","Callability_Analysis.generate_gene_summary":"${true}","Callability_Analysis.target_bed":"gs://fc-8123e6b7-c245-489c-9a28-5ebbd128458d/redo_analysis/16bp_padded_nurture_CDS.hg38.bed","Callability_Analysis.min_base_quality":"${20}","Callability_Analysis.output_prefix":"Nurture","Callability_Analysis.bai_or_crai_paths":"${this.samples.crai}","Callability_Analysis.sample_ids":"${this.samples.sample_id}","Callability_Analysis.ref_fasta":"${workspace.referenceData_hg38_ref_fasta}","Callability_Analysis.gene_bed":"gs://gptag/AnnotateBed/bed_for_all_gene.hg38.bed","Callability_Analysis.low_coverage_threshold":"${20}"}

CallabilityAnalysis/Callability_Analysis_update.wdl

@@ -612,6 +612,7 @@ task concatenate_results {
         String output_prefix
         Int memory_gb = 16
         Int disk_size = 32
+        String? docker_override
     }
     command {
         python3 /scripts/aggregation_script.hg38.py --clinvar_file ~{clinvar_annotation} --samtools_coverage_file ~{samtools_coverage_file} --annotation_file ~{annotation_file} --output_prefix ~{output_prefix}