Reverted changes to vapor inputs

broadinstitute · Dec 4, 2024 · 4a27320 · 4a27320
1 parent 30e1cb6
commit 4a27320
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Showing 4 changed files with 15 additions and 1 deletion.
diff --git a/inputs/templates/test/Vapor/Vapor.json.tmpl b/inputs/templates/test/Vapor/Vapor.json.tmpl
@@ -4,6 +4,8 @@
     "Vapor.vapor_docker": {{ dockers.vapor_docker | tojson }},
     "Vapor.contigs": {{ reference_resources.primary_contigs_list | tojson }},
     "Vapor.ref_fasta" : {{ reference_resources.reference_fasta | tojson }},
+    "Vapor.ref_fai" : {{ reference_resources.reference_index | tojson }},
+    "Vapor.ref_dict": {{ reference_resources.reference_dict | tojson }},
     "Vapor.save_plots": "false",
 
     "Vapor.prefix": {{ test_batch.example_pacbio_sample_id | tojson }},

diff --git a/inputs/templates/test/Vapor/VaporBatch.json.tmpl b/inputs/templates/test/Vapor/VaporBatch.json.tmpl
@@ -4,6 +4,8 @@
     "VaporBatch.vapor_docker": {{ dockers.vapor_docker | tojson }},
     "VaporBatch.contigs": {{ reference_resources.primary_contigs_list | tojson }},
     "VaporBatch.ref_fasta" : {{ reference_resources.reference_fasta | tojson }},
+    "VaporBatch.ref_fai" : {{ reference_resources.reference_index | tojson }},
+    "VaporBatch.ref_dict": {{ reference_resources.reference_dict | tojson }},
     "VaporBatch.save_plots": "false",
 
     "VaporBatch.samples": {{ test_batch.pacbio_samples | tojson }},

diff --git a/wdl/Vapor.wdl b/wdl/Vapor.wdl
@@ -14,6 +14,8 @@ workflow Vapor {
     Boolean save_plots  # Control whether plots are final output
 
     File ref_fasta
+    File ref_fai
+    File ref_dict
     File contigs
 
     String vapor_docker
@@ -50,6 +52,8 @@ workflow Vapor {
         bam_or_cram_index = bam_or_cram_index,
         bed = PreprocessBedForVapor.contig_bed,
         ref_fasta = ref_fasta,
+        ref_fai = ref_fai,
+        ref_dict = ref_dict,
         vapor_docker = vapor_docker,
         runtime_attr_override = runtime_attr_vapor
     }
@@ -78,6 +82,8 @@ task RunVaporWithCram {
     String bam_or_cram_index
     File bed
     File ref_fasta
+    File ref_fai
+    File ref_dict
     String vapor_docker
     RuntimeAttr? runtime_attr_override
   }
@@ -129,4 +135,4 @@ task RunVaporWithCram {
     preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }
-}
+}
diff --git a/wdl/VaporBatch.wdl b/wdl/VaporBatch.wdl
@@ -11,6 +11,8 @@ workflow VaporBatch {
     File bed_file  # Multi-sample bed file, generated with svtk vcf2bed (e.g. as in MainVcfQc)
 
     File ref_fasta
+    File ref_fai
+    File ref_dict
     File contigs
 
     String vapor_docker
@@ -35,6 +37,8 @@ workflow VaporBatch {
         bed_file = bed_file,
         sample_id = samples[i],
         ref_fasta = ref_fasta,
+        ref_fai = ref_fai,
+        ref_dict = ref_dict,
         contigs = contigs,
         save_plots = save_plots,
         vapor_docker = vapor_docker,