Module name defenestration (#213)

Rename modules to be more descriptive. See PR comment for old => new naming key
broadinstitute · Aug 16, 2021 · f0771a6 · f0771a6
1 parent 4e2dd28
commit f0771a6
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Showing 152 changed files with 2,677 additions and 3,008 deletions.
diff --git a/README.md b/README.md
diff --git a/input_templates/GATKSVPipelineBatch.ref_panel_1kg.json.tmpl b/input_templates/GATKSVPipelineBatch.ref_panel_1kg.json.tmpl
@@ -8,7 +8,7 @@
 
   "GATKSVPipelineBatch.batch": {{ ref_panel.batch_name | tojson }},
   "GATKSVPipelineBatch.ped_file": {{ ref_panel.ped_file | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.requester_pays_crams": {{ ref_panel.requester_pays_crams | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.requester_pays_crams": {{ ref_panel.requester_pays_crams | tojson }},
   "GATKSVPipelineBatch.sample_ids": {{ ref_panel.samples | tojson }},
   "GATKSVPipelineBatch.bam_or_cram_files": {{ ref_panel.bam_or_cram_files | tojson }},
   "GATKSVPipelineBatch.gvcfs": {{ ref_panel.gvcfs | tojson }},
@@ -43,15 +43,15 @@
   "GATKSVPipelineBatch.primary_contigs_fai" : {{ reference_resources.primary_contigs_fai | tojson }},
   "GATKSVPipelineBatch.genome_file" : {{ reference_resources.genome_file | tojson }},
 
-  "GATKSVPipelineBatch.Module00aBatch.reference_version": {{ reference_resources.reference_version | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.delly_exclude_intervals_file": {{ reference_resources.delly_exclude_intervals_file | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.wham_include_list_bed_file": {{ reference_resources.wham_include_list_bed_file | tojson }},
-  "GATKSVPipelineBatch.Module00aBatch.preprocessed_intervals": {{ reference_resources.preprocessed_intervals | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.reference_version": {{ reference_resources.reference_version | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.delly_exclude_intervals_file": {{ reference_resources.delly_exclude_intervals_file | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.manta_region_bed": {{ reference_resources.manta_region_bed | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.melt_standard_vcf_header": {{ reference_resources.melt_std_vcf_header | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.wham_include_list_bed_file": {{ reference_resources.wham_include_list_bed_file | tojson }},
+  "GATKSVPipelineBatch.GatherSampleEvidenceBatch.preprocessed_intervals": {{ reference_resources.preprocessed_intervals | tojson }},
 
-  "GATKSVPipelineBatch.Module00b.wgd_scoring_mask": {{ reference_resources.wgd_scoring_mask | tojson }},
-  "GATKSVPipelineBatch.Module00b.run_vcf_qc": "false",
+  "GATKSVPipelineBatch.EvidenceQC.wgd_scoring_mask": {{ reference_resources.wgd_scoring_mask | tojson }},
+  "GATKSVPipelineBatch.EvidenceQC.run_vcf_qc": "false",
 
   "GATKSVPipelineBatch.GATKSVPipelinePhase1.unpadded_intervals_file" : {{ reference_resources.unpadded_intervals_file | tojson }},
   "GATKSVPipelineBatch.GATKSVPipelinePhase1.dbsnp_vcf" : {{ reference_resources.dbsnp_vcf | tojson }},
@@ -107,29 +107,29 @@
   "GATKSVPipelineBatch.GATKSVPipelinePhase1.outlier_cutoff_table" : {{ ref_panel.outlier_cutoff_table | tojson }},
   "GATKSVPipelineBatch.GATKSVPipelinePhase1.outlier_cutoff_nIQR": "999999",
 
-  "GATKSVPipelineBatch.Module04.n_RD_genotype_bins": "100000",
-  "GATKSVPipelineBatch.Module04.n_per_split": "5000",
-  "GATKSVPipelineBatch.Module04.pesr_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
-  "GATKSVPipelineBatch.Module04.seed_cutoffs": {{ reference_resources.seed_cutoffs | tojson }},
-  "GATKSVPipelineBatch.Module04.reference_build": "hg38",
-  "GATKSVPipelineBatch.Module04.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
-
-  "GATKSVPipelineBatch.Module04b.n_RdTest_bins": "100000",
-  "GATKSVPipelineBatch.Module04b.n_per_split": "5000",
-
-  "GATKSVPipelineBatch.Module0506.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
-  "GATKSVPipelineBatch.Module0506.empty_file" : {{ reference_resources.empty_file | tojson }},
-  "GATKSVPipelineBatch.Module0506.cytobands": {{ reference_resources.cytobands | tojson }},
-  "GATKSVPipelineBatch.Module0506.mei_bed": {{ reference_resources.mei_bed | tojson }},
-  "GATKSVPipelineBatch.Module0506.pe_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
-  "GATKSVPipelineBatch.Module0506.depth_exclude_list": {{ reference_resources.depth_exclude_list | tojson }},
-  "GATKSVPipelineBatch.Module0506.min_sr_background_fail_batches": 0.5,
-  "GATKSVPipelineBatch.Module0506.max_shards_per_chrom_clean_vcf_step1": 200,
-  "GATKSVPipelineBatch.Module0506.min_records_per_shard_clean_vcf_step1": 5000,
-  "GATKSVPipelineBatch.Module0506.samples_per_clean_vcf_step2_shard": 100,
-  "GATKSVPipelineBatch.Module0506.random_seed": 0,
-  "GATKSVPipelineBatch.Module0506.max_shards_per_chrom": 100,
-  "GATKSVPipelineBatch.Module0506.min_variants_per_shard": 30,
+  "GATKSVPipelineBatch.GenotypeBatch.n_RD_genotype_bins": "100000",
+  "GATKSVPipelineBatch.GenotypeBatch.n_per_split": "5000",
+  "GATKSVPipelineBatch.GenotypeBatch.pesr_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
+  "GATKSVPipelineBatch.GenotypeBatch.seed_cutoffs": {{ reference_resources.seed_cutoffs | tojson }},
+  "GATKSVPipelineBatch.GenotypeBatch.reference_build": "hg38",
+  "GATKSVPipelineBatch.GenotypeBatch.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
+
+  "GATKSVPipelineBatch.RegenotypeCNVs.n_RdTest_bins": "100000",
+  "GATKSVPipelineBatch.RegenotypeCNVs.n_per_split": "5000",
+
+  "GATKSVPipelineBatch.MakeCohortVcf.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.empty_file" : {{ reference_resources.empty_file | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.cytobands": {{ reference_resources.cytobands | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.mei_bed": {{ reference_resources.mei_bed | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.pe_exclude_list": {{ reference_resources.pesr_exclude_list | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.depth_exclude_list": {{ reference_resources.depth_exclude_list | tojson }},
+  "GATKSVPipelineBatch.MakeCohortVcf.min_sr_background_fail_batches": 0.5,
+  "GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
+  "GATKSVPipelineBatch.MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
+  "GATKSVPipelineBatch.MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
+  "GATKSVPipelineBatch.MakeCohortVcf.random_seed": 0,
+  "GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom": 100,
+  "GATKSVPipelineBatch.MakeCohortVcf.min_variants_per_shard": 30,
 
   "GATKSVPipelineBatch.BatchQC.qc_definitions" : "gs://gatk-sv-resources-public/test/batch/batch_sv.test_large.qc_definitions.tsv",