Multiple declarations of primary_contigs_fai (#225)

* multiple declarations of primary_contigs_fai * remove duplicated gcnv_copy_number_posterior_expectation_mode
broadinstitute · Sep 14, 2021 · 74693ff · 74693ff
1 parent 9e44979
commit 74693ff
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Showing 5 changed files with 2 additions and 7 deletions.
diff --git a/input_templates/TrainGCNV.ref_panel_1kg.json.tmpl b/input_templates/TrainGCNV.ref_panel_1kg.json.tmpl
@@ -40,7 +40,6 @@
   "TrainGCNV.gcnv_model_convergence_snr_averaging_window" : 500,
   "TrainGCNV.gcnv_model_convergence_snr_countdown_window" : 10,
   "TrainGCNV.gcnv_model_cnv_coherence_length" : 1000,
-  "TrainGCNV.gcnv_copy_number_posterior_expectation_mode" : "EXACT",
 
   "TrainGCNV.gcnv_learning_rate" : 0.03,
   "TrainGCNV.gcnv_num_thermal_advi_iters" : 250,

diff --git a/input_templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl b/input_templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl
@@ -40,7 +40,6 @@
   "TrainGCNV.gcnv_model_convergence_snr_averaging_window" : 500,
   "TrainGCNV.gcnv_model_convergence_snr_countdown_window" : 10,
   "TrainGCNV.gcnv_model_cnv_coherence_length" : 1000,
-  "TrainGCNV.gcnv_copy_number_posterior_expectation_mode" : "EXACT",
 
   "TrainGCNV.gcnv_learning_rate" : 0.03,
   "TrainGCNV.gcnv_num_thermal_advi_iters" : 250,

diff --git a/test_input_templates/TrainGCNV/TrainGCNV.json.tmpl b/test_input_templates/TrainGCNV/TrainGCNV.json.tmpl
@@ -40,7 +40,6 @@
   "TrainGCNV.gcnv_model_convergence_snr_averaging_window" : 500,
   "TrainGCNV.gcnv_model_convergence_snr_countdown_window" : 10,
   "TrainGCNV.gcnv_model_cnv_coherence_length" : 1000,
-  "TrainGCNV.gcnv_copy_number_posterior_expectation_mode" : "EXACT",
 
   "TrainGCNV.gcnv_learning_rate" : 0.03,
   "TrainGCNV.gcnv_num_thermal_advi_iters" : 250,

diff --git a/wdl/GatherSampleEvidence.wdl b/wdl/GatherSampleEvidence.wdl
@@ -24,7 +24,7 @@ workflow GatherSampleEvidence {
     # Use to revise Y, R, W, S, K, M, D, H, V, B, X bases in BAM to N. Use only if providing a CRAM file as input 
     # May be more expensive - use only if necessary
     Boolean revise_base_cram_to_bam = false
-    File? primary_contigs_fai # required if using revise_base_cram_to_bam
+    File? primary_contigs_fai # required if using revise_base_cram_to_bam (or if run_module_metrics = true)
 
     # Note: raw and "safe" CRAM/BAM IDs can be generated with GetSampleID
     String sample_id
@@ -77,7 +77,6 @@ workflow GatherSampleEvidence {
     # Run module metrics workflow at the end - on by default
     Boolean? run_module_metrics
     String? sv_pipeline_base_docker  # required if run_module_metrics = true
-    File? primary_contigs_fai  # required if run_module_metrics = true
     File? baseline_delly_vcf  # baseline files are optional for metrics workflow
     File? baseline_manta_vcf
     File? baseline_wham_vcf

diff --git a/wdl/GatherSampleEvidenceBatch.wdl b/wdl/GatherSampleEvidenceBatch.wdl
@@ -15,7 +15,7 @@ workflow GatherSampleEvidenceBatch {
     # Use to revise Y, R, W, S, K, M, D, H, V, B, X bases in BAM to N. Use only if providing a CRAM file as input 
     # May be more expensive - use only if necessary
     Boolean revise_base_cram_to_bam = false
-    File? primary_contigs_fai # required if using revise_base_cram_to_bam
+    File? primary_contigs_fai # required if using revise_base_cram_to_bam (or if run_module_metrics = true)
 
     # Caller flags
     Boolean collect_coverage = true
@@ -67,7 +67,6 @@ workflow GatherSampleEvidenceBatch {
     String? batch  # required if run_module_metrics = true
     String? sv_pipeline_base_docker  # required if run_module_metrics = true
     String? linux_docker  # required if run_module_metrics = true
-    File? primary_contigs_fai  # required if run_module_metrics = true
     File? baseline_delly_vcf  # baseline files are optional for metrics workflow
     File? baseline_manta_vcf
     File? baseline_wham_vcf