fix: elevate disk_size params to workflow level

workflows/reference/gatk-reference.wdl

@@ -14,23 +14,28 @@ workflow gatk_reference {
             dbSNP_vcf: "dbSNP VCF file for the reference genome.",
             dbSNP_vcf_index: "Index for the dbSNP VCF file for the reference genome.",
             interval_list: "List of intervals that will be used when computing variants.",
-            known_vcfs: "VCF files with known variants to use with variant calling."
+            known_vcfs: "VCF files with known variants to use with variant calling.",
         }
         allowNestedInputs: true
     }
 
     parameter_meta {
+        known_vcf_urls: "URLs from which to retrieve VCF files with known variants."
+        known_vcf_names: "Names of the VCF files with known variants. Order should match that of `known_vcf_urls`."
         reference_fa_url: "URL from which to retrieve the reference FASTA file."
         reference_fa_name: "Name of the output reference FASTA file."
         reference_fa_md5: "MD5 checksum for the reference FASTA file."
         dbSNP_vcf_url: "URL from which to retrieve the dbSNP VCF file."
         dbSNP_vcf_name: "Name of the dbSNP VCF file."
+        known_vcf_disk_size_gb: "Disk size (in GB) to allocate for downloading the VCF files with known variants."
+        reference_fa_disk_size_gb: "Disk size (in GB) to allocate for downloading the reference FASTA file."
+        dbSNP_vcf_disk_size_gb: "Disk size (in GB) to allocate for downloading the dbSNP VCF file."
         dbSNP_vcf_index_url: "URL from which to retrieve the index for the dbSNP VCF file."
         dbSNP_vcf_index_name: "Name of the index for the dbSNP VCF file."
-        known_vcf_urls: "URLs from which to retrieve VCF files with known variants."
-        known_vcf_names: "Names of the VCF files with known variants. Order should match that of `known_vcf_urls`."
         interval_list_url: "URL from which to retrieve the list of intervals to use when computing variants."
         interval_list_name: "Name of the list of intervals to use when computing variants."
+        dbSNP_vcf_index_disk_size_gb: "Disk size (in GB) to allocate for downloading the index for the dbSNP VCF file."
+        interval_list_disk_size_gb: "Disk size (in GB) to allocate for downloading the list of intervals to use when computing variants."
     }
 
     input {
@@ -43,51 +48,63 @@ workflow gatk_reference {
         String dbSNP_vcf_url
         #@ except: SnakeCase
         String dbSNP_vcf_name
+        Int known_vcf_disk_size_gb
+        Int reference_fa_disk_size_gb
+        #@ except: SnakeCase
+        Int dbSNP_vcf_disk_size_gb
         #@ except: SnakeCase
         String? dbSNP_vcf_index_url
         #@ except: SnakeCase
         String? dbSNP_vcf_index_name
         String? interval_list_url
         String? interval_list_name
+        #@ except: SnakeCase
+        Int? dbSNP_vcf_index_disk_size_gb
+        Int? interval_list_disk_size_gb
     }
 
     call util.download as fasta_download { input:
         url = reference_fa_url,
         outfile_name = reference_fa_name,
-        md5sum = reference_fa_md5
+        md5sum = reference_fa_md5,
+        disk_size_gb = reference_fa_disk_size_gb,
     }
 
     call samtools.faidx { input:
-        fasta = fasta_download.downloaded_file
+        fasta = fasta_download.downloaded_file,
     }
 
     call picard.create_sequence_dictionary { input:
-        fasta = fasta_download.downloaded_file
+        fasta = fasta_download.downloaded_file,
     }
 
     call util.download as dbsnp { input:
         url = dbSNP_vcf_url,
-        outfile_name = dbSNP_vcf_name
+        outfile_name = dbSNP_vcf_name,
+        disk_size_gb = dbSNP_vcf_disk_size_gb,
     }
 
     if (defined(dbSNP_vcf_index_url) && defined(dbSNP_vcf_index_name)) {
         call util.download as dbsnp_index { input:
             url = select_first([dbSNP_vcf_index_url, "undefined"]),
-            outfile_name = select_first([dbSNP_vcf_index_name, "undefined"])
+            outfile_name = select_first([dbSNP_vcf_index_name, "undefined"]),
+            disk_size_gb = select_first([dbSNP_vcf_index_disk_size_gb, 1]),
         }
     }
 
     if (defined(interval_list_url) && defined(interval_list_name)) {
         call util.download as intervals { input:
             url = select_first([interval_list_url, "undefined"]),
-            outfile_name = select_first([interval_list_name, "undefined"])
+            outfile_name = select_first([interval_list_name, "undefined"]),
+            disk_size_gb = select_first([interval_list_disk_size_gb, 1]),
         }
     }
 
     scatter (pair in zip(known_vcf_urls, known_vcf_names)) {
         call util.download as known_vcf { input:
             url = pair.left,
-            outfile_name = pair.right
+            outfile_name = pair.right,
+            disk_size_gb = known_vcf_disk_size_gb,
         }
     }
 

workflows/reference/make-qc-reference.wdl

@@ -81,9 +81,9 @@ workflow make_qc_reference {
             "UTR",
         ]
         Boolean protein = false
-        Int kraken_fastas_disk_size_gb = 10
         Int reference_fa_disk_size_gb = 10
         Int gtf_disk_size_gb = 10
+        Int kraken_fastas_disk_size_gb = 10
     }
 
     call util.download as reference_download { input: