Added official json that can run on Terra

broadinstitute · Nov 14, 2023 · b90311e · b90311e
1 parent 048a4ba
commit b90311e
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Showing 7 changed files with 119 additions and 191 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -21,12 +21,12 @@ workflows:
    subclass: WDL
    primaryDescriptorPath: /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.wdl
    testParameterFiles:
-   - /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json
+   - /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow_terra.inputs.json
  - name: mutect2-gatk4
    subclass: WDL
    primaryDescriptorPath: /GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4.wdl
    testParameterFiles:
-   - /Users/gaoyueya/Documents/GitHub/TAG-public/GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4.inputs.json
+   - /GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4_terra.inputs.json
  - name: GenerateDuplexConsensusBams
    subclass: WDL
    primaryDescriptorPath: /Liquid_Biopsy_Duplex_Analysis/GenerateDuplexConsensusBams/GenerateDuplexConsensusBams.wdl

diff --git a/GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json b/GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json
diff --git a/GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow_terra.inputs.json b/GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow_terra.inputs.json
@@ -0,0 +1,82 @@
+{
+    "CNVSomaticPairWorkflow.CallCopyRatioSegmentsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.CallCopyRatioSegmentsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.CollectAllelicCountsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.CollectAllelicCountsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.CollectCountsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.CollectCountsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.DenoiseReadCountsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.DenoiseReadCountsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsNormal.min_total_allele_count_normal": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsNormal.normal_allelic_counts": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsNormal.output_dir": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.ModelSegmentsTumor.output_dir": "${}",
+    "CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosNormal.output_dir": "${}",
+    "CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.PlotDenoisedCopyRatiosTumor.output_dir": "${}",
+    "CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.cpu": "${}",
+    "CNVSomaticPairWorkflow.PlotModeledSegmentsNormal.output_dir": "${}",
+    "CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.cpu": "${}",
+    "CNVSomaticPairWorkflow.PlotModeledSegmentsTumor.output_dir": "${}",
+    "CNVSomaticPairWorkflow.PreprocessIntervals.cpu": "${}",
+    "CNVSomaticPairWorkflow.additional_args_for_oncotator": "${}",
+    "CNVSomaticPairWorkflow.bin_length": "${0}",
+    "CNVSomaticPairWorkflow.blacklist_intervals": "${workspace.blacklist_intervals}",
+    "CNVSomaticPairWorkflow.boot_disk_space_gb_for_oncotator": "${}",
+    "CNVSomaticPairWorkflow.calling_copy_ratio_z_score_threshold": "${3.05}",
+    "CNVSomaticPairWorkflow.collect_counts_format": "${}",
+    "CNVSomaticPairWorkflow.common_sites": "${workspace.common_sites}",
+    "CNVSomaticPairWorkflow.emergency_extra_disk": "${}",
+    "CNVSomaticPairWorkflow.gatk4_jar_override": "${}",
+    "CNVSomaticPairWorkflow.gatk_docker": "us.gcr.io/broad-gatk/gatk:4.2.3.0",
+    "CNVSomaticPairWorkflow.genotyping_base_error_rate": "${}",
+    "CNVSomaticPairWorkflow.genotyping_homozygous_log_ratio_threshold": "${}",
+    "CNVSomaticPairWorkflow.intervals": "${workspace.CNV_intervals}",
+    "CNVSomaticPairWorkflow.is_run_oncotator": "${true}",
+    "CNVSomaticPairWorkflow.kernel_approximation_dimension": "${}",
+    "CNVSomaticPairWorkflow.kernel_scaling_allele_fraction": "${}",
+    "CNVSomaticPairWorkflow.kernel_variance_allele_fraction": "${}",
+    "CNVSomaticPairWorkflow.kernel_variance_copy_ratio": "${}",
+    "CNVSomaticPairWorkflow.max_num_segments_per_chromosome": "${}",
+    "CNVSomaticPairWorkflow.max_num_smoothing_iterations": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_call_copy_ratio_segments": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_collect_allelic_counts": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_collect_counts": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_denoise_read_counts": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_model_segments": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_oncotator": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_plotting": "${}",
+    "CNVSomaticPairWorkflow.mem_gb_for_preprocess_intervals": "${}",
+    "CNVSomaticPairWorkflow.min_total_allele_count": "${}",
+    "CNVSomaticPairWorkflow.min_total_allele_count_normal": "${}",
+    "CNVSomaticPairWorkflow.minimum_base_quality": "${}",
+    "CNVSomaticPairWorkflow.minimum_contig_length": "${}",
+    "CNVSomaticPairWorkflow.minor_allele_fraction_prior_alpha": "${}",
+    "CNVSomaticPairWorkflow.neutral_segment_copy_ratio_lower_bound": "${}",
+    "CNVSomaticPairWorkflow.neutral_segment_copy_ratio_upper_bound": "${}",
+    "CNVSomaticPairWorkflow.normal_bam": "${}",
+    "CNVSomaticPairWorkflow.normal_bam_idx": "${}",
+    "CNVSomaticPairWorkflow.num_burn_in_allele_fraction": "${}",
+    "CNVSomaticPairWorkflow.num_burn_in_copy_ratio": "${}",
+    "CNVSomaticPairWorkflow.num_changepoints_penalty_factor": "${}",
+    "CNVSomaticPairWorkflow.num_samples_allele_fraction": "${}",
+    "CNVSomaticPairWorkflow.num_samples_copy_ratio": "${}",
+    "CNVSomaticPairWorkflow.num_smoothing_iterations_per_fit": "${}",
+    "CNVSomaticPairWorkflow.number_of_eigensamples": "${}",
+    "CNVSomaticPairWorkflow.oncotator_docker": "broadinstitute/oncotator:1.9.5.0-eval-gatk-protected",
+    "CNVSomaticPairWorkflow.outlier_neutral_segment_copy_ratio_z_score_threshold": "${}",
+    "CNVSomaticPairWorkflow.padding": "${}",
+    "CNVSomaticPairWorkflow.preemptible_attempts": "${}",
+    "CNVSomaticPairWorkflow.read_count_pon": "${workspace.read_count_pon}",
+    "CNVSomaticPairWorkflow.ref_fasta": "${workspace.ref_fasta}",
+    "CNVSomaticPairWorkflow.ref_fasta_dict": "${workspace.ref_dict}",
+    "CNVSomaticPairWorkflow.ref_fasta_fai": "${workspace.ref_fasta_index}",
+    "CNVSomaticPairWorkflow.smoothing_threshold_allele_fraction": "${}",
+    "CNVSomaticPairWorkflow.smoothing_threshold_copy_ratio": "${}",
+    "CNVSomaticPairWorkflow.tumor_bam": "${this.cram_or_bam_path}",
+    "CNVSomaticPairWorkflow.tumor_bam_idx": "${this.crai_or_bai_path}",
+    "CNVSomaticPairWorkflow.window_sizes": "${}"
+}
diff --git a/GATK_CNV_Mutect2/M2-CNV-DataAnalysis-workspace-attributes.tsv b/GATK_CNV_Mutect2/M2-CNV-DataAnalysis-workspace-attributes.tsv
@@ -0,0 +1,2 @@
+workspace:m2_pon	ref_fasta_index	variants_for_contamination_index	gnomad_index	variants_for_contamination	onco_ds_tar_gz	common_sites	intervals	read_count_pon	gnomad	ref_dict	m2_pon_index	ref_fasta	CNV_intervals	blacklist_intervals
+gs://fc-secure-5268d48f-5b0c-495e-a371-b5846c6ea94d/M2_gatk-4.0.4.0_TWIST_hg19_PON.82_hardClipped_normals.Dec2020.vcf	gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai	gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx	gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx	gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf	gs://gatk-best-practices/somatic-b37/oncotator_v1_ds_April052016.tar.gz	gs://gptag/somatic/aux/common_sites/common_snps.interval_list	gs://gptag/somatic/aux/common_sites/broad_custom_exome_v1.Homo_sapiens_assembly19.targets.interval_list	gs://fc-secure-5268d48f-5b0c-495e-a371-b5846c6ea94d/TWIST_82_normals.gcCorrected_blacklisted.gatk4.1.2.0_cnv_pon.Nov2020.pon.hdf5	gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf	gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict	gs://fc-secure-5268d48f-5b0c-495e-a371-b5846c6ea94d/M2_gatk-4.0.4.0_TWIST_hg19_PON.82_hardClipped_normals.Dec2020.vcf.idx	gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta	gs://fc-secure-5268d48f-5b0c-495e-a371-b5846c6ea94d/intervals/broad_custom_exome_v1.Homo_sapiens_assembly19_CNV.targets.interval_list	gs://gptag/somatic/aux/common_sites/CNV_and_centromere_blacklist.hg19.list
diff --git a/GATK_CNV_Mutect2/mutect2-gatk4/README.md b/GATK_CNV_Mutect2/mutect2-gatk4/README.md
@@ -49,3 +49,5 @@ This WDL workflow runs GATK4 Mutect2 on a single tumor-normal pair or on a singl
 * MutationalBurden: task reads MAF and computes both coding and non-coding mutational burdens (# of mutations / callable bases)
 * LegoPlot: task generates lego plots
 
+### Log
+v1.1.2: Update the original workflow to [GATK4.1.8.1 official workflow](https://raw.githubusercontent.com/broadinstitute/gatk/4.1.8.1/scripts/mutect2_wdl/mutect2.wdl).