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Update CNV and M2 to GATK official workflows #38

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merged 1 commit into from
Aug 9, 2023
Merged

Update CNV and M2 to GATK official workflows #38

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4 changes: 2 additions & 2 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,9 @@ workflows:
- /CollectSamError/CollectSamErrorMetrics.inputs.json
- name: GATK4_CNV
subclass: WDL
primaryDescriptorPath: /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNV.wdl
primaryDescriptorPath: /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.wdl
testParameterFiles:
- /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNV.terra-inputs.json
- /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json
- name: mutect2-gatk4
subclass: WDL
primaryDescriptorPath: /GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4.wdl
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1 change: 0 additions & 1 deletion GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNV.terra-inputs.json
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119 changes: 119 additions & 0 deletions GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,119 @@
{
"CNVSomaticPairWorkflow.preemptible_attempts": "Int? (optional)",
"CNVSomaticPairWorkflow.oncotator_docker": "String? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_call_copy_ratio_segments": "Int? (optional)",
"CNVSomaticPairWorkflow.num_smoothing_iterations_per_fit": "Int? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsNormal.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_funcotator": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.calling_copy_ratio_z_score_threshold": "Float? (optional)",
"CNVSomaticPairWorkflow.minor_allele_fraction_prior_alpha": "Float? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsTumor.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.funcotator_ref_version": "String? (optional)",
"CNVSomaticPairWorkflow.gatk_docker": "String",
"CNVSomaticPairWorkflow.num_changepoints_penalty_factor": "Float? (optional)",
"CNVSomaticPairWorkflow.common_sites": "File",
"CNVSomaticPairWorkflow.tumor_bam_idx": "File",
"CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_oncotator": "Int? (optional)",
"CNVSomaticPairWorkflow.neutral_segment_copy_ratio_upper_bound": "Float? (optional)",
"CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.CollectCountsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.minimum_base_quality": "String? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_denoise_read_counts": "Int? (optional)",
"CNVSomaticPairWorkflow.min_total_allele_count_normal": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.genotyping_base_error_rate": "Float? (optional)",
"CNVSomaticPairWorkflow.DenoiseReadCountsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.funcotator_cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.funcotator_is_removing_untared_datasources": "Boolean? (optional)",
"CNVSomaticPairWorkflow.emergency_extra_disk": "Int? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.CallCopyRatioSegmentsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsNormal.normal_allelic_counts": "File? (optional)",
"CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.funcotator_excluded_fields": "Array[String]? (optional)",
"CNVSomaticPairWorkflow.point_size_copy_ratio": "Float? (optional)",
"CNVSomaticPairWorkflow.ref_fasta_fai": "File",
"CNVSomaticPairWorkflow.CollectCountsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.kernel_approximation_dimension": "Int? (optional)",
"CNVSomaticPairWorkflow.outlier_neutral_segment_copy_ratio_z_score_threshold": "Float? (optional)",
"CNVSomaticPairWorkflow.funcotator_annotation_overrides": "Array[String]? (optional)",
"CNVSomaticPairWorkflow.kernel_variance_copy_ratio": "Float? (optional)",
"CNVSomaticPairWorkflow.CallCopyRatioSegmentsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.funcotator_disk_space_gb": "Int? (optional)",
"CNVSomaticPairWorkflow.additional_args_for_oncotator": "String? (optional)",
"CNVSomaticPairWorkflow.funcotator_transcript_selection_list": "File? (optional)",
"CNVSomaticPairWorkflow.DenoiseReadCountsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.mem_gb_for_model_segments": "Int? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_plotting": "Int? (optional)",
"CNVSomaticPairWorkflow.min_total_allele_count": "Int? (optional)",
"CNVSomaticPairWorkflow.point_size_allele_fraction": "Float? (optional)",
"CNVSomaticPairWorkflow.ref_fasta": "File",
"CNVSomaticPairWorkflow.ModelSegmentsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.num_burn_in_allele_fraction": "Int? (optional)",
"CNVSomaticPairWorkflow.smoothing_threshold_allele_fraction": "Float? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.mem_gb_for_collect_counts": "Int? (optional)",
"CNVSomaticPairWorkflow.ref_fasta_dict": "File",
"CNVSomaticPairWorkflow.collect_counts_format": "String? (optional)",
"CNVSomaticPairWorkflow.minimum_contig_length": "Int? (optional)",
"CNVSomaticPairWorkflow.maximum_copy_ratio": "String? (optional)",
"CNVSomaticPairWorkflow.is_run_funcotator": "Boolean? (optional)",
"CNVSomaticPairWorkflow.smoothing_threshold_copy_ratio": "Float? (optional)",
"CNVSomaticPairWorkflow.ModelSegmentsNormal.min_total_allele_count_normal": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.tumor_bam": "File",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.normal_bam_idx": "File? (optional)",
"CNVSomaticPairWorkflow.CollectAllelicCountsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.neutral_segment_copy_ratio_lower_bound": "Float? (optional)",
"CNVSomaticPairWorkflow.num_samples_allele_fraction": "Int? (optional)",
"CNVSomaticPairWorkflow.funcotator_annotation_defaults": "Array[String]? (optional)",
"CNVSomaticPairWorkflow.max_num_segments_per_chromosome": "Int? (optional)",
"CNVSomaticPairWorkflow.blacklist_intervals": "File? (optional)",
"CNVSomaticPairWorkflow.CallCopyRatioSegmentsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.kernel_scaling_allele_fraction": "Float? (optional)",
"CNVSomaticPairWorkflow.CollectCountsNormal.disabled_read_filters": "Array[String]? (optional)",
"CNVSomaticPairWorkflow.funcotator_use_ssd": "Boolean? (optional)",
"CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.mem_gb_for_preprocess_intervals": "Int? (optional)",
"CNVSomaticPairWorkflow.genotyping_homozygous_log_ratio_threshold": "Float? (optional)",
"CNVSomaticPairWorkflow.CollectAllelicCountsNormal.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.max_num_smoothing_iterations": "Int? (optional)",
"CNVSomaticPairWorkflow.PreprocessIntervals.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosTumor.output_dir": "String? (optional)",
"CNVSomaticPairWorkflow.funcotator_transcript_selection_mode": "String? (optional)",
"CNVSomaticPairWorkflow.is_run_oncotator": "Boolean? (optional)",
"CNVSomaticPairWorkflow.padding": "Int? (optional)",
"CNVSomaticPairWorkflow.PreprocessIntervals.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.mem_gb_for_collect_allelic_counts": "Int? (optional)",
"CNVSomaticPairWorkflow.normal_bam": "File? (optional)",
"CNVSomaticPairWorkflow.gcs_project_for_requester_pays": "String? (optional)",
"CNVSomaticPairWorkflow.CollectCountsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.CollectAllelicCountsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.num_burn_in_copy_ratio": "Int? (optional)",
"CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.DenoiseReadCountsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.CollectAllelicCountsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.CNVFuncotateSegmentsWorkflow.interval_list": "File? (optional)",
"CNVSomaticPairWorkflow.intervals": "File",
"CNVSomaticPairWorkflow.funcotator_data_sources_tar_gz": "File? (optional)",
"CNVSomaticPairWorkflow.gatk4_jar_override": "File? (optional)",
"CNVSomaticPairWorkflow.CollectCountsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.CallCopyRatioSegmentsNormal.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.DenoiseReadCountsTumor.cpu": "Int? (optional)",
"CNVSomaticPairWorkflow.number_of_eigensamples": "Int? (optional)",
"CNVSomaticPairWorkflow.CollectCountsTumor.disabled_read_filters": "Array[String]? (optional)",
"CNVSomaticPairWorkflow.window_sizes": "Array[Int]+? (optional, default = [8, 16, 32, 64, 128, 256])",
"CNVSomaticPairWorkflow.num_samples_copy_ratio": "Int? (optional)",
"CNVSomaticPairWorkflow.read_count_pon": "File",
"CNVSomaticPairWorkflow.ModelSegmentsTumor.use_ssd": "Boolean (optional, default = false)",
"CNVSomaticPairWorkflow.boot_disk_space_gb_for_oncotator": "Int? (optional)",
"CNVSomaticPairWorkflow.bin_length": "Int? (optional)",
"CNVSomaticPairWorkflow.additional_args_for_funcotator": "String? (optional)",
"CNVSomaticPairWorkflow.kernel_variance_allele_fraction": "Float? (optional)"
}

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