add noAddress: true to runtime blocks for airgap-safe tasks

Adds noAddress: true to the runtime block of all WDL tasks that do not
require internet access. Tasks that need network (NCBI downloads/uploads,
Terra API calls, Nextstrain dataset fetches, GISAID uploads, pangolin,
snpEff, kraken2 db builds) are left unchanged. This Cromwell/Terra
runtime attribute prevents allocation of a public IP address to task VMs,
improving security posture and reducing costs.

Author: dpark01

pipes/WDL/tasks/tasks_16S_amplicon.wdl

@@ -65,6 +65,7 @@ task qiime_import_from_bam {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 }
 
@@ -146,6 +147,7 @@ task trim_reads {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 }
 
@@ -196,6 +198,7 @@ task join_paired_ends {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 }
 
@@ -271,6 +274,7 @@ task deblur {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 }
 task train_classifier {
@@ -359,6 +363,7 @@ task train_classifier {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 }
 task tax_analysis {
@@ -422,5 +427,6 @@ task tax_analysis {
         cpu: cpu
         disk: "~{disk_size_gb} GB"
         disks: "local-disk ~{disk_size_gb} HDD"
+        noAddress: true
     }
 } 

pipes/WDL/tasks/tasks_assembly.wdl

@@ -107,6 +107,7 @@ task assemble {
         disks: "local-disk ~{disk_size} SSD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x8"
+        noAddress: true
     }
 
 }
@@ -197,6 +198,7 @@ task select_references {
     disk: "~{disk_size} GB" # TESs
     dx_instance_type: "mem1_ssd1_v2_x2"
     preemptible: 2
+    noAddress: true
   }
 }
 
@@ -459,6 +461,7 @@ task scaffold {
         disks: "local-disk ~{disk_size} SSD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x8"
+        noAddress: true
     }
 }
 
@@ -544,6 +547,7 @@ task skani_triangle {
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x4"
     preemptible: 2
+    noAddress: true
   }
 }
 
@@ -626,6 +630,7 @@ task ivar_trim {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x4"
+        noAddress: true
     }
 }
 
@@ -691,6 +696,7 @@ task ivar_trim_stats {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB"
         dx_instance_type: "mem1_ssd1_v2_x2"
+        noAddress: true
     }
 }
 
@@ -859,6 +865,7 @@ task align_reads {
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x8"
     preemptible: 1
+    noAddress: true
   }
 }
 
@@ -999,6 +1006,7 @@ task refine_assembly_with_aligned_reads {
         disks: "local-disk ~{disk_size} SSD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x8"
+        noAddress: true
     }
 }
 
@@ -1120,6 +1128,7 @@ task run_discordance {
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x2"
         preemptible: 1
+        noAddress: true
     }
 }
 
@@ -1231,6 +1240,7 @@ task filter_bad_ntc_batches {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x2"
+        noAddress: true
     }
     output {
         File           seqids_kept      = "seqids.filtered.txt"
@@ -1341,5 +1351,6 @@ task wgsim {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x2"
+        noAddress: true
     }
 }

pipes/WDL/tasks/tasks_demux.wdl

@@ -38,6 +38,7 @@ task merge_tarballs {
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd2_v2_x16"
     preemptible: 0
+    noAddress: true
   }
 }
 
@@ -90,6 +91,7 @@ task samplesheet_rename_ids {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -134,6 +136,7 @@ task revcomp_i5 {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB"
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -653,6 +656,7 @@ task illumina_demux {
     dx_instance_type: "mem3_ssd2_v2_x32"
     dx_timeout: "20H"
     preemptible: 0  # this is the very first operation before scatter, so let's get it done quickly & reliably
+    noAddress: true
   }
 }
 
@@ -685,6 +689,7 @@ task map_map_setdefault {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB"
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -716,6 +721,7 @@ task merge_maps {
     disks: "local-disk ~{disk_size} LOCAL"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -804,6 +810,7 @@ task group_fastq_pairs {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -862,6 +869,7 @@ task get_illumina_run_metadata {
     disks: "local-disk ~{disk_size} LOCAL"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -900,6 +908,7 @@ task check_for_barcode3 {
     docker: docker
     memory: "1 GB"
     cpu: 1
+    noAddress: true
   }
 }
 
@@ -1036,6 +1045,7 @@ task demux_fastqs {
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x16"
     preemptible: 0  # this is the very first operation before scatter, so let's get it done quickly & reliably
+    noAddress: true
   }
 }
 
@@ -1083,6 +1093,7 @@ task merge_demux_metrics {
     disks: "local-disk 50 HDD"
     disk: "50 GB"
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -1150,5 +1161,6 @@ task merge_sample_metadata {
     disks: "local-disk 50 HDD"
     disk: "50 GB"
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }

pipes/WDL/tasks/tasks_interhost.wdl

@@ -133,6 +133,7 @@ task subsample_by_cases {
         disks:  "local-disk 200 HDD"
         disk:   "200 GB"
         dx_instance_type: "mem3_ssd1_v2_x4"
+        noAddress: true
     }
     output {
         File    genome_matrix_days              =   "genome_matrix_days.tsv"
@@ -194,6 +195,7 @@ task multi_align_mafft_ref {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem3_ssd1_v2_x8"
+    noAddress: true
   }
 }
 
@@ -239,6 +241,7 @@ task multi_align_mafft {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem2_ssd1_v2_x8"
+    noAddress: true
   }
 }
 
@@ -339,6 +342,7 @@ task beast {
     gpuType:             select_first([gpu_type, "nvidia-tesla-p4"])  # Terra
     gpuCount:            select_first([gpu_count, 1])  # Terra
     nvidiaDriverVersion: "410.79"
+    noAddress: true
   }
 }
 
@@ -376,6 +380,7 @@ task index_ref {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
 
+    noAddress: true
   }
 }
 
@@ -405,6 +410,7 @@ task trimal_clean_msa {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x8"
+    noAddress: true
   }
 }
 
@@ -461,6 +467,7 @@ task merge_vcfs_bcftools {
     memory: "~{select_first([machine_mem_gb, 3])} GB"
     cpu: 2
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -522,6 +529,7 @@ task merge_vcfs_gatk {
     memory: "~{select_first([machine_mem_gb, 3])} GB"
     cpu: 2
     dx_instance_type: "mem1_ssd1_v2_x2"
+    noAddress: true
   }
 }
 
@@ -591,5 +599,6 @@ task reconstructr {
     disk: "~{disk_size} GB" # TES
     bootDiskSizeGb: 50
     dx_instance_type: "mem1_ssd1_v2_x4"
+    noAddress: true
   }
 }

pipes/WDL/tasks/tasks_intrahost.wdl

@@ -126,6 +126,7 @@ task polyphonia_detect_cross_contamination {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x4"
+    noAddress: true
   }
 }
 
@@ -201,6 +202,7 @@ task lofreq {
     disks: "local-disk ~{disk_size} SSD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x4"
+    noAddress: true
   }
 }
 
@@ -241,6 +243,7 @@ task isnvs_per_sample {
     docker: docker
     memory: "~{select_first([machine_mem_gb, 7])} GB"
     dx_instance_type: "mem1_ssd1_v2_x8"
+    noAddress: true
   }
 }
 

pipes/WDL/tasks/tasks_megablast.wdl

@@ -56,6 +56,7 @@ task trim_rmdup_subsamp {
         cpu:    cpu
         disks: "local-disk ~{disk_size_gb} LOCAL"
         dx_instance_type: "n2-highmem-4"
+        noAddress: true
     }
 }
 
@@ -154,6 +155,7 @@ task lca_megablast {
         disks: "local-disk ~{disk_size_gb} HDD"
 
         dx_instance_type: "n2-highmem-16"
+        noAddress: true
     }
 }
 
@@ -233,6 +235,7 @@ task ChunkBlastHits {
         disks: "local-disk ~{disk_size_gb} LOCAL"
 
         dx_instance_type: "n2-standard-16"
+        noAddress: true
     }
 }
 
@@ -406,5 +409,6 @@ task blastoff {
         disks: "local-disk ~{disk_size_gb} HDD"
 
         dx_instance_type: "n2-highmem-8"
+        noAddress: true
     }
 }