Making the Vapor plots optional to store as a final output (#692)

* added boolean and modified output of plots to be optional and output only if the boolean is true * changed boolean name, modified output to be NONE_FILE if set to false * tried to change optional files output format * try to address checking issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * address issue * modified jsons * made edits based on review * made edits based on review
broadinstitute · Jul 3, 2024 · 7e7f2f7 · 7e7f2f7
1 parent dc88507
commit 7e7f2f7
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Showing 4 changed files with 23 additions and 14 deletions.
diff --git a/inputs/templates/test/Vapor/Vapor.json.tmpl b/inputs/templates/test/Vapor/Vapor.json.tmpl
@@ -6,6 +6,7 @@
  "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 }},
  "Vapor.sample_id": {{ 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
@@ -6,6 +6,7 @@
  "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 }},
  "VaporBatch.bam_or_cram_files": {{ test_batch.pacbio_crams | tojson }},

diff --git a/wdl/Vapor.wdl b/wdl/Vapor.wdl
@@ -11,6 +11,8 @@ workflow Vapor {
  File bed_file
  String sample_id
 
+ Boolean save_plots # Control whether plots are final output
+
  File ref_fasta
  File ref_fai
  File ref_dict
@@ -20,15 +22,17 @@ workflow Vapor {
  String sv_base_mini_docker
  String sv_pipeline_docker
 
- RuntimeAttr? runtime_attr_vapor 
+ RuntimeAttr? runtime_attr_vapor
  RuntimeAttr? runtime_attr_bcf2vcf
  RuntimeAttr? runtime_attr_vcf2bed
  RuntimeAttr? runtime_attr_split_vcf
  RuntimeAttr? runtime_attr_concat_beds
  RuntimeAttr? runtime_attr_LocalizeCram
+
+ File? NONE_FILE_ # Create a null file - do not use this input
  }
 
- scatter ( contig in read_lines(contigs) ) {
+ scatter (contig in read_lines(contigs)) {
 
  call tasks10.PreprocessBedForVapor {
  input:
@@ -57,16 +61,16 @@ workflow Vapor {
 
  call tasks10.ConcatVapor {
  input:
- shard_bed_files=RunVaporWithCram.vapor,
- shard_plots=RunVaporWithCram.vapor_plot,
- prefix=prefix,
- sv_base_mini_docker=sv_base_mini_docker,
- runtime_attr_override=runtime_attr_concat_beds
+ shard_bed_files = RunVaporWithCram.vapor,
+ shard_plots = RunVaporWithCram.vapor_plot,
+ prefix = prefix,
+ sv_base_mini_docker = sv_base_mini_docker,
+ runtime_attr_override = runtime_attr_concat_beds
  }
 
  output {
  File vapor_bed = ConcatVapor.merged_bed_file
- File vapor_plots = ConcatVapor.merged_bed_plot
+ File? vapor_plots = if save_plots then ConcatVapor.merged_bed_plot else NONE_FILE_
  }
 }
 
@@ -85,8 +89,8 @@ task RunVaporWithCram {
  }
 
  RuntimeAttr default_attr = object {
- cpu_cores: 1, 
- mem_gb: 15, 
+ cpu_cores: 1,
+ mem_gb: 15,
  disk_gb: 30,
  boot_disk_gb: 10,
  preemptible_tries: 3,
@@ -107,8 +111,8 @@ task RunVaporWithCram {
  export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token`
  samtools view -h -T ~{ref_fasta} -o ~{contig}.bam ~{bam_or_cram_file} ~{contig}
  samtools index ~{contig}.bam
- 
- #run vapor
+
+ # run vapor
  mkdir ~{prefix}.~{contig}
 
  vapor bed \
@@ -120,7 +124,7 @@ task RunVaporWithCram {
  --pacbio-input ~{contig}.bam
 
  tar -czf ~{prefix}.~{contig}.tar.gz ~{prefix}.~{contig}
- bgzip  ~{prefix}.~{contig}.vapor
+ bgzip ~{prefix}.~{contig}.vapor
  >>>
  runtime {
  cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])

diff --git a/wdl/VaporBatch.wdl b/wdl/VaporBatch.wdl
@@ -19,6 +19,8 @@ workflow VaporBatch {
  String sv_base_mini_docker
  String sv_pipeline_docker
 
+ Boolean save_plots
+
  RuntimeAttr? runtime_attr_vapor
  RuntimeAttr? runtime_attr_bcf2vcf
  RuntimeAttr? runtime_attr_vcf2bed
@@ -38,6 +40,7 @@ workflow VaporBatch {
  ref_fai = ref_fai,
  ref_dict = ref_dict,
  contigs = contigs,
+ save_plots = save_plots,
  vapor_docker = vapor_docker,
  sv_base_mini_docker = sv_base_mini_docker,
  sv_pipeline_docker = sv_pipeline_docker,
@@ -50,7 +53,7 @@ workflow VaporBatch {
  }
  output {
  Array[File] vapor_batch_beds = Vapor.vapor_bed
- Array[File] vapor_batch_plots = Vapor.vapor_plots
+ Array[File?] vapor_batch_plots = Vapor.vapor_plots
  }
 }