Merge pull request #994 from broadinstitute/dp-dxwdl

dpark01 · web-flow · commit 83a5fabb8b98 · 2019-10-16T16:52:41.000-04:00
dxWDL upgrade
diff --git a/pipes/WDL/dx-launcher/demux_launcher.yml b/pipes/WDL/dx-launcher/demux_launcher.yml
@@ -177,7 +177,7 @@ runSpec:
         fi
         for i in $(seq "$lane_count"); do
           folder2=$(printf "%s/%s/reads/L%d" "$folder" "$run_id" $i)
-          runcmd="dx run $demux_workflow_id -i stage-1.flowcell_tgz=$run_tarball -i illumina_demux.lane=$i -i illumina_demux.maxReadsInRamPerTile=$max_reads_in_ram_per_tile -i illumina_demux.maxRecordsInRam=$max_records_in_ram -i illumina_demux.minimumBaseQuality=$min_base_quality -i illumina_demux.threads=$demux_threads $sequencing_center_input --folder $folder2 --instance-type illumina_demux=$demux_instance_type --name demux:$run_id:L$i -y --brief"
+          runcmd="dx run $demux_workflow_id -i stage-0.flowcell_tgz=$run_tarball -i illumina_demux.lane=$i -i illumina_demux.maxReadsInRamPerTile=$max_reads_in_ram_per_tile -i illumina_demux.maxRecordsInRam=$max_records_in_ram -i illumina_demux.minimumBaseQuality=$min_base_quality -i illumina_demux.threads=$demux_threads $sequencing_center_input --folder $folder2 --instance-type illumina_demux=$demux_instance_type --name demux:$run_id:L$i -y --brief"
           echo "$runcmd"
           set +x
           if [ -n "$api_token" ]; then
diff --git a/pipes/WDL/workflows/tasks/tasks_assembly.wdl b/pipes/WDL/workflows/tasks/tasks_assembly.wdl
@@ -83,7 +83,7 @@ task assemble {
         docker: "quay.io/broadinstitute/viral-ngs"
         memory: "15 GB"
         cpu: 4
-        dx_instance_type: "mem1_ssd1_x8"
+        dx_instance_type: "mem1_ssd1_v2_x8"
     }
 
 }
@@ -167,7 +167,7 @@ task scaffold {
         docker: "quay.io/broadinstitute/viral-ngs"
         memory: "15 GB"
         cpu: 4
-        dx_instance_type: "mem1_ssd1_x8"
+        dx_instance_type: "mem1_ssd1_v2_x8"
     }
 }
 
@@ -224,7 +224,7 @@ task refine {
         docker: "quay.io/broadinstitute/viral-ngs"
         memory: "7 GB"
         cpu: 8
-        dx_instance_type: "mem1_ssd1_x8"
+        dx_instance_type: "mem1_ssd1_v2_x8"
     }
 }
 
@@ -365,7 +365,7 @@ task refine_2x_and_plot {
         docker: "quay.io/broadinstitute/viral-ngs"
         memory: "7 GB"
         cpu: 8
-        dx_instance_type: "mem1_ssd1_x8"
+        dx_instance_type: "mem1_ssd1_v2_x8"
     }
 }
 
diff --git a/pipes/WDL/workflows/tasks/tasks_demux.wdl b/pipes/WDL/workflows/tasks/tasks_demux.wdl
@@ -22,7 +22,7 @@
 #    docker: "quay.io/broadinstitute/viral-ngs"
 #    memory: "7 GB"
 #    cpu: 4
-#    dx_instance_type: "mem1_hdd2_x8"
+#    dx_instance_type: "mem2_hdd2_v2_x4"
 #    preemptible: 0  # this is the very first operation before scatter, so let's get it done quickly & reliably
 #  }
 #}
@@ -201,7 +201,7 @@ task illumina_demux {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "16 GB"
     cpu: 36
-    dx_instance_type: "mem1_ssd2_x36"
+    dx_instance_type: "mem1_ssd2_v2_x36"
     preemptible: 0  # this is the very first operation before scatter, so let's get it done quickly & reliably
   }
 }
@@ -238,7 +238,7 @@ task merge_and_reheader_bams {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "2000 MB"
     cpu: 2
-    dx_instance_type: "mem1_ssd2_x4"
+    dx_instance_type: "mem1_ssd2_v2_x4"
   }
 }
 
diff --git a/pipes/WDL/workflows/tasks/tasks_interhost.wdl b/pipes/WDL/workflows/tasks/tasks_interhost.wdl
@@ -31,7 +31,7 @@ task multi_align_mafft_ref {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "7 GB"
     cpu: 8
-    dx_instance_type: "mem1_ssd1_x8"
+    dx_instance_type: "mem1_ssd1_v2_x8"
   }
 }
 
@@ -66,7 +66,7 @@ task multi_align_mafft {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "7 GB"
     cpu: 8
-    dx_instance_type: "mem1_ssd1_x8"
+    dx_instance_type: "mem1_ssd1_v2_x8"
   }
 }
 
diff --git a/pipes/WDL/workflows/tasks/tasks_metagenomics.wdl b/pipes/WDL/workflows/tasks/tasks_metagenomics.wdl
@@ -68,7 +68,7 @@ task krakenuniq {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "200 GB"
     cpu: 32
-    dx_instance_type: "mem3_ssd1_x32"
+    dx_instance_type: "mem3_ssd1_v2_x32"
     preemptible: 0
   }
 }
@@ -108,7 +108,7 @@ task krona {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "4 GB"
     cpu: 1
-    dx_instance_type: "mem1_ssd2_x2"
+    dx_instance_type: "mem1_ssd2_v2_x2"
   }
 }
 
@@ -166,7 +166,7 @@ task filter_bam_to_taxa {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "4 GB"
     cpu: 1
-    dx_instance_type: "mem1_ssd2_x2"
+    dx_instance_type: "mem1_ssd2_v2_x2"
   }
 
 }
@@ -233,6 +233,6 @@ task kaiju {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "100 GB"
     cpu: 16
-    dx_instance_type: "mem3_ssd1_x16"
+    dx_instance_type: "mem3_ssd1_v2_x16"
   }
 }
diff --git a/pipes/WDL/workflows/tasks/tasks_ncbi.wdl b/pipes/WDL/workflows/tasks/tasks_ncbi.wdl
@@ -20,7 +20,7 @@ task download_fasta {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x2"
+    dx_instance_type: "mem1_ssd1_v2_x2"
   }
 }
 
@@ -55,7 +55,7 @@ task download_annotations {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x2"
+    dx_instance_type: "mem1_ssd1_v2_x2"
   }
 }
 
@@ -84,20 +84,20 @@ task annot_transfer {
   }
 
   output {
-    Array[File]+ transferred_feature_tables = glob("*.tbl")
+    Array[File]  transferred_feature_tables = glob("*.tbl")
     String       viralngs_version           = "viral-ngs_version_unknown"
   }
   runtime {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x2"
+    dx_instance_type: "mem1_ssd1_v2_x2"
   }
 }
 
 task prepare_genbank {
   Array[File]+ assemblies_fasta
-  Array[File]+ annotations_tbl
+  Array[File]  annotations_tbl
   File         authors_sbt
   File         biosampleMap
   File         genbankSourceTable
@@ -140,7 +140,7 @@ task prepare_genbank {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x2"
+    dx_instance_type: "mem1_ssd1_v2_x2"
   }
 }
 
diff --git a/pipes/WDL/workflows/tasks/tasks_read_utils.wdl b/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
@@ -33,7 +33,7 @@ task downsample_bams {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x4"
+    dx_instance_type: "mem1_ssd1_v2_x4"
   }
 }
 
diff --git a/pipes/WDL/workflows/tasks/tasks_reports.wdl b/pipes/WDL/workflows/tasks/tasks_reports.wdl
@@ -110,7 +110,7 @@ task plot_coverage {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "3500 MB"
     cpu: 4
-    dx_instance_type: "mem1_ssd1_x8"
+    dx_instance_type: "mem1_ssd1_v2_x8"
   }
 }
 
@@ -135,7 +135,7 @@ task coverage_report {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "2000 MB"
     cpu: 2
-    dx_instance_type: "mem1_ssd2_x4"
+    dx_instance_type: "mem1_ssd2_v2_x4"
   }
 }
 
@@ -159,7 +159,7 @@ task fastqc {
     memory: "2 GB"
     cpu: 1
     docker: "quay.io/broadinstitute/viral-ngs"
-    dx_instance_type: "mem1_ssd1_x4"
+    dx_instance_type: "mem1_ssd1_v2_x4"
   }
 }
 
@@ -197,7 +197,7 @@ task spikein_report {
     memory: "3 GB"
     cpu: 2
     docker: "quay.io/broadinstitute/viral-ngs"
-    dx_instance_type: "mem1_ssd1_x4"
+    dx_instance_type: "mem1_ssd1_v2_x4"
   }
 }
 
@@ -223,7 +223,7 @@ task spikein_summary {
     memory: "3 GB"
     cpu: 2
     docker: "quay.io/broadinstitute/viral-ngs"
-    dx_instance_type: "mem1_ssd1_x4"
+    dx_instance_type: "mem1_ssd1_v2_x4"
   }
 }
 
@@ -256,7 +256,7 @@ task aggregate_metagenomics_reports {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "4 GB"
     cpu: 1
-    dx_instance_type: "mem1_ssd2_x2"
+    dx_instance_type: "mem1_ssd2_v2_x2"
     preemptible: 0
   }
 }
diff --git a/pipes/WDL/workflows/tasks/tasks_taxon_filter.wdl b/pipes/WDL/workflows/tasks/tasks_taxon_filter.wdl
@@ -71,7 +71,7 @@ task deplete_taxa {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "14 GB"
     cpu: 8
-    dx_instance_type: "mem1_ssd1_x16"
+    dx_instance_type: "mem1_ssd1_v2_x16"
     preemptible: 0
   }
 }
@@ -130,7 +130,7 @@ task filter_to_taxon {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "14 GB"
     cpu: 16
-    dx_instance_type: "mem1_ssd1_x8"
+    dx_instance_type: "mem1_ssd1_v2_x8"
   }
 }
 
@@ -153,7 +153,7 @@ task build_lastal_db {
     docker: "quay.io/broadinstitute/viral-ngs"
     memory: "7 GB"
     cpu: 2
-    dx_instance_type: "mem1_ssd1_x4"
+    dx_instance_type: "mem1_ssd1_v2_x4"
   }
 }
 
@@ -194,7 +194,7 @@ task merge_one_per_sample {
     memory: "7 GB"
     cpu: 4
     docker: "quay.io/broadinstitute/viral-ngs"
-    dx_instance_type: "mem1_ssd2_x4"
+    dx_instance_type: "mem1_ssd1_v2_x16"
   }
 }
 
diff --git a/test/input/WDL/test_inputs-assemble_denovo_with_deplete-dnanexus.dx.json b/test/input/WDL/test_inputs-assemble_denovo_with_deplete-dnanexus.dx.json
@@ -1,13 +1,13 @@
 {
-	"stage-1.raw_reads_unmapped_bam": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F8F2kVQ09y3Q9Qj14fF806q2" } },
+	"stage-0.raw_reads_unmapped_bam": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F8F2kVQ09y3Q9Qj14fF806q2" } },
 
-	"stage-1.bmtaggerDbs": [
+	"stage-0.bmtaggerDbs": [
 		{ "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-BYF6g8Q0zjF77x79bGYgJ1Zb" } }
 	],
 
-	"stage-2.lastal_db_fasta": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } },
-	"stage-4.reference_genome_fasta": [ { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } } ],
+	"stage-1.lastal_db_fasta": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } },
+	"stage-3.reference_genome_fasta": [ { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F1zXZ9Q0pvkp7FkZ646YJX2y" } } ],
 
-	"stage-5.gatk_jar": { "$dnanexus_link": { "project": "project-F89kXY805X08BpXq7xjxbX9F", "id": "file-F89Vx8Q09y3VFxf1KKXbbVv4" } },
-	"stage-5.novocraft_license": { "$dnanexus_link": { "project": "project-F89kXY805X08BpXq7xjxbX9F", "id": "file-F1zkVGQ0jy1P68J88kyJ8zVF" } }
+	"stage-4.gatk_jar": { "$dnanexus_link": { "project": "project-F89kXY805X08BpXq7xjxbX9F", "id": "file-F89Vx8Q09y3VFxf1KKXbbVv4" } },
+	"stage-4.novocraft_license": { "$dnanexus_link": { "project": "project-F89kXY805X08BpXq7xjxbX9F", "id": "file-F1zkVGQ0jy1P68J88kyJ8zVF" } }
 }
diff --git a/test/input/WDL/test_inputs-demux_plus-dnanexus.dx.json b/test/input/WDL/test_inputs-demux_plus-dnanexus.dx.json
@@ -1,16 +1,16 @@
 {
-  "stage-0.bmtaggerDbs": [
+  "stage-common.bmtaggerDbs": [
   { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-BYF6g8Q0zjF77x79bGYgJ1Zb" } }
   ],
-  "stage-0.blastDbs": [
+  "stage-common.blastDbs": [
   { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-BzBpkK80x0z8GBQPfZ4kgPKp" } }
   ],
 
-  "stage-1.flowcell_tgz": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F86qY0j09y3Q5FbKKK3k4gzq" } },
-  "stage-1.samplesheet":  { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F8F32gQ09y3VJ4kjBzvgZkKv" } },
-  "stage-1.maxMismatches": 0,
-  "stage-1.minimumQuality": 25,
+  "stage-0.flowcell_tgz": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F86qY0j09y3Q5FbKKK3k4gzq" } },
+  "stage-0.samplesheet":  { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F8F32gQ09y3VJ4kjBzvgZkKv" } },
+  "stage-0.maxMismatches": 0,
+  "stage-0.minimumQuality": 25,
 
-  "stage-3.krakenuniq_db_tar_lz4": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-FVYQqP006zFF064QBGf022X1" } },
-  "stage-3.krona_taxonomy_db_tgz": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F4z0fgj07FZ8jg8yP7yz0Qzb" } }
+  "stage-5.krakenuniq_db_tar_lz4": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-FVYQqP006zFF064QBGf022X1" } },
+  "stage-5.krona_taxonomy_db_tgz": { "$dnanexus_link": { "project": "project-F8PQ6380xf5bK0Qk0YPjB17P", "id": "file-F4z0fgj07FZ8jg8yP7yz0Qzb" } }
 }
diff --git a/travis/install-wdl.sh b/travis/install-wdl.sh
@@ -17,11 +17,11 @@ cached_fetch_jar_from_github () {
 	ln -s $CACHE_DIR/$_jar_fname $_tool_name.jar
 }
 
-cached_fetch_jar_from_github broadinstitute cromwell womtool 33.1
-cached_fetch_jar_from_github broadinstitute cromwell cromwell 33.1
-cached_fetch_jar_from_github dnanexus dxWDL dxWDL 0.72
+cached_fetch_jar_from_github broadinstitute cromwell womtool 47
+cached_fetch_jar_from_github broadinstitute cromwell cromwell 47
+cached_fetch_jar_from_github dnanexus dxWDL dxWDL v1.33
 
-TGZ=dx-toolkit-v0.285.0-ubuntu-16.04-amd64.tar.gz
+TGZ=dx-toolkit-v0.288.0-ubuntu-16.04-amd64.tar.gz
 if [ ! -f $CACHE_DIR/$TGZ ]; then
 	echo "Fetching $TGZ"
 	wget --quiet https://dnanexus-sdk.s3.amazonaws.com/$TGZ
diff --git a/travis/version-wdl-runtimes.sh b/travis/version-wdl-runtimes.sh
@@ -10,7 +10,7 @@ sed -i -- "s|$OLD_TAG|$NEW_TAG|g" pipes/WDL/workflows/tasks/*.wdl
 CURRENT_VERSION=`echo "$NEW_TAG" | cut -d\: -f2`
 VERSION_PLACEHOLDER="viral-ngs_version_unknown"
 
-echo Replacing $VERSION_PLACEHOLDER with $CURENT_VERSION in all task WDL files
+echo Replacing $VERSION_PLACEHOLDER with $CURRENT_VERSION in all task WDL files
 sed -i -- "s|$VERSION_PLACEHOLDER|$CURRENT_VERSION|g" pipes/WDL/workflows/tasks/*.wdl
 
 #echo "DEBUG: here are the modified runtime lines:"

Original file line number	Diff line number	Diff line change
`@@ -83,7 +83,7 @@ task assemble {`
`83`	`83`	`docker: "quay.io/broadinstitute/viral-ngs"`
`84`	`84`	`memory: "15 GB"`
`85`	`85`	`cpu: 4`
`86`		`- dx_instance_type: "mem1_ssd1_x8"`
	`86`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`87`	`87`	`}`
`88`	`88`
`89`	`89`	`}`
`@@ -167,7 +167,7 @@ task scaffold {`
`167`	`167`	`docker: "quay.io/broadinstitute/viral-ngs"`
`168`	`168`	`memory: "15 GB"`
`169`	`169`	`cpu: 4`
`170`		`- dx_instance_type: "mem1_ssd1_x8"`
	`170`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`171`	`171`	`}`
`172`	`172`	`}`
`173`	`173`
`@@ -224,7 +224,7 @@ task refine {`
`224`	`224`	`docker: "quay.io/broadinstitute/viral-ngs"`
`225`	`225`	`memory: "7 GB"`
`226`	`226`	`cpu: 8`
`227`		`- dx_instance_type: "mem1_ssd1_x8"`
	`227`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`228`	`228`	`}`
`229`	`229`	`}`
`230`	`230`
`@@ -365,7 +365,7 @@ task refine_2x_and_plot {`
`365`	`365`	`docker: "quay.io/broadinstitute/viral-ngs"`
`366`	`366`	`memory: "7 GB"`
`367`	`367`	`cpu: 8`
`368`		`- dx_instance_type: "mem1_ssd1_x8"`
	`368`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`369`	`369`	`}`
`370`	`370`	`}`
`371`	`371`
Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`	`# docker: "quay.io/broadinstitute/viral-ngs"`
`23`	`23`	`# memory: "7 GB"`
`24`	`24`	`# cpu: 4`
`25`		`-# dx_instance_type: "mem1_hdd2_x8"`
	`25`	`+# dx_instance_type: "mem2_hdd2_v2_x4"`
`26`	`26`	`# preemptible: 0 # this is the very first operation before scatter, so let's get it done quickly & reliably`
`27`	`27`	`# }`
`28`	`28`	`#}`
`@@ -201,7 +201,7 @@ task illumina_demux {`
`201`	`201`	`docker: "quay.io/broadinstitute/viral-ngs"`
`202`	`202`	`memory: "16 GB"`
`203`	`203`	`cpu: 36`
`204`		`- dx_instance_type: "mem1_ssd2_x36"`
	`204`	`+ dx_instance_type: "mem1_ssd2_v2_x36"`
`205`	`205`	`preemptible: 0 # this is the very first operation before scatter, so let's get it done quickly & reliably`
`206`	`206`	`}`
`207`	`207`	`}`
`@@ -238,7 +238,7 @@ task merge_and_reheader_bams {`
`238`	`238`	`docker: "quay.io/broadinstitute/viral-ngs"`
`239`	`239`	`memory: "2000 MB"`
`240`	`240`	`cpu: 2`
`241`		`- dx_instance_type: "mem1_ssd2_x4"`
	`241`	`+ dx_instance_type: "mem1_ssd2_v2_x4"`
`242`	`242`	`}`
`243`	`243`	`}`
`244`	`244`
Original file line number	Diff line number	Diff line change
`@@ -31,7 +31,7 @@ task multi_align_mafft_ref {`
`31`	`31`	`docker: "quay.io/broadinstitute/viral-ngs"`
`32`	`32`	`memory: "7 GB"`
`33`	`33`	`cpu: 8`
`34`		`- dx_instance_type: "mem1_ssd1_x8"`
	`34`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`35`	`35`	`}`
`36`	`36`	`}`
`37`	`37`
`@@ -66,7 +66,7 @@ task multi_align_mafft {`
`66`	`66`	`docker: "quay.io/broadinstitute/viral-ngs"`
`67`	`67`	`memory: "7 GB"`
`68`	`68`	`cpu: 8`
`69`		`- dx_instance_type: "mem1_ssd1_x8"`
	`69`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`70`	`70`	`}`
`71`	`71`	`}`
`72`	`72`
Original file line number	Diff line number	Diff line change
`@@ -68,7 +68,7 @@ task krakenuniq {`
`68`	`68`	`docker: "quay.io/broadinstitute/viral-ngs"`
`69`	`69`	`memory: "200 GB"`
`70`	`70`	`cpu: 32`
`71`		`- dx_instance_type: "mem3_ssd1_x32"`
	`71`	`+ dx_instance_type: "mem3_ssd1_v2_x32"`
`72`	`72`	`preemptible: 0`
`73`	`73`	`}`
`74`	`74`	`}`
`@@ -108,7 +108,7 @@ task krona {`
`108`	`108`	`docker: "quay.io/broadinstitute/viral-ngs"`
`109`	`109`	`memory: "4 GB"`
`110`	`110`	`cpu: 1`
`111`		`- dx_instance_type: "mem1_ssd2_x2"`
	`111`	`+ dx_instance_type: "mem1_ssd2_v2_x2"`
`112`	`112`	`}`
`113`	`113`	`}`
`114`	`114`
`@@ -166,7 +166,7 @@ task filter_bam_to_taxa {`
`166`	`166`	`docker: "quay.io/broadinstitute/viral-ngs"`
`167`	`167`	`memory: "4 GB"`
`168`	`168`	`cpu: 1`
`169`		`- dx_instance_type: "mem1_ssd2_x2"`
	`169`	`+ dx_instance_type: "mem1_ssd2_v2_x2"`
`170`	`170`	`}`
`171`	`171`
`172`	`172`	`}`
`@@ -233,6 +233,6 @@ task kaiju {`
`233`	`233`	`docker: "quay.io/broadinstitute/viral-ngs"`
`234`	`234`	`memory: "100 GB"`
`235`	`235`	`cpu: 16`
`236`		`- dx_instance_type: "mem3_ssd1_x16"`
	`236`	`+ dx_instance_type: "mem3_ssd1_v2_x16"`
`237`	`237`	`}`
`238`	`238`	`}`
Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,7 @@ task download_fasta {`
`20`	`20`	`docker: "quay.io/broadinstitute/viral-ngs"`
`21`	`21`	`memory: "3 GB"`
`22`	`22`	`cpu: 2`
`23`		`- dx_instance_type: "mem1_ssd1_x2"`
	`23`	`+ dx_instance_type: "mem1_ssd1_v2_x2"`
`24`	`24`	`}`
`25`	`25`	`}`
`26`	`26`
`@@ -55,7 +55,7 @@ task download_annotations {`
`55`	`55`	`docker: "quay.io/broadinstitute/viral-ngs"`
`56`	`56`	`memory: "3 GB"`
`57`	`57`	`cpu: 2`
`58`		`- dx_instance_type: "mem1_ssd1_x2"`
	`58`	`+ dx_instance_type: "mem1_ssd1_v2_x2"`
`59`	`59`	`}`
`60`	`60`	`}`
`61`	`61`
`@@ -84,20 +84,20 @@ task annot_transfer {`
`84`	`84`	`}`
`85`	`85`
`86`	`86`	`output {`
`87`		`- Array[File]+ transferred_feature_tables = glob("*.tbl")`
	`87`	`+ Array[File] transferred_feature_tables = glob("*.tbl")`
`88`	`88`	`String viralngs_version = "viral-ngs_version_unknown"`
`89`	`89`	`}`
`90`	`90`	`runtime {`
`91`	`91`	`docker: "quay.io/broadinstitute/viral-ngs"`
`92`	`92`	`memory: "3 GB"`
`93`	`93`	`cpu: 2`
`94`		`- dx_instance_type: "mem1_ssd1_x2"`
	`94`	`+ dx_instance_type: "mem1_ssd1_v2_x2"`
`95`	`95`	`}`
`96`	`96`	`}`
`97`	`97`
`98`	`98`	`task prepare_genbank {`
`99`	`99`	`Array[File]+ assemblies_fasta`
`100`		`- Array[File]+ annotations_tbl`
	`100`	`+ Array[File] annotations_tbl`
`101`	`101`	`File authors_sbt`
`102`	`102`	`File biosampleMap`
`103`	`103`	`File genbankSourceTable`
`@@ -140,7 +140,7 @@ task prepare_genbank {`
`140`	`140`	`docker: "quay.io/broadinstitute/viral-ngs"`
`141`	`141`	`memory: "3 GB"`
`142`	`142`	`cpu: 2`
`143`		`- dx_instance_type: "mem1_ssd1_x2"`
	`143`	`+ dx_instance_type: "mem1_ssd1_v2_x2"`
`144`	`144`	`}`
`145`	`145`	`}`
`146`	`146`
Original file line number	Diff line number	Diff line change
`@@ -33,7 +33,7 @@ task downsample_bams {`
`33`	`33`	`docker: "quay.io/broadinstitute/viral-ngs"`
`34`	`34`	`memory: "3 GB"`
`35`	`35`	`cpu: 2`
`36`		`- dx_instance_type: "mem1_ssd1_x4"`
	`36`	`+ dx_instance_type: "mem1_ssd1_v2_x4"`
`37`	`37`	`}`
`38`	`38`	`}`
`39`	`39`
Original file line number	Diff line number	Diff line change
`@@ -110,7 +110,7 @@ task plot_coverage {`
`110`	`110`	`docker: "quay.io/broadinstitute/viral-ngs"`
`111`	`111`	`memory: "3500 MB"`
`112`	`112`	`cpu: 4`
`113`		`- dx_instance_type: "mem1_ssd1_x8"`
	`113`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`114`	`114`	`}`
`115`	`115`	`}`
`116`	`116`
`@@ -135,7 +135,7 @@ task coverage_report {`
`135`	`135`	`docker: "quay.io/broadinstitute/viral-ngs"`
`136`	`136`	`memory: "2000 MB"`
`137`	`137`	`cpu: 2`
`138`		`- dx_instance_type: "mem1_ssd2_x4"`
	`138`	`+ dx_instance_type: "mem1_ssd2_v2_x4"`
`139`	`139`	`}`
`140`	`140`	`}`
`141`	`141`
`@@ -159,7 +159,7 @@ task fastqc {`
`159`	`159`	`memory: "2 GB"`
`160`	`160`	`cpu: 1`
`161`	`161`	`docker: "quay.io/broadinstitute/viral-ngs"`
`162`		`- dx_instance_type: "mem1_ssd1_x4"`
	`162`	`+ dx_instance_type: "mem1_ssd1_v2_x4"`
`163`	`163`	`}`
`164`	`164`	`}`
`165`	`165`
`@@ -197,7 +197,7 @@ task spikein_report {`
`197`	`197`	`memory: "3 GB"`
`198`	`198`	`cpu: 2`
`199`	`199`	`docker: "quay.io/broadinstitute/viral-ngs"`
`200`		`- dx_instance_type: "mem1_ssd1_x4"`
	`200`	`+ dx_instance_type: "mem1_ssd1_v2_x4"`
`201`	`201`	`}`
`202`	`202`	`}`
`203`	`203`
`@@ -223,7 +223,7 @@ task spikein_summary {`
`223`	`223`	`memory: "3 GB"`
`224`	`224`	`cpu: 2`
`225`	`225`	`docker: "quay.io/broadinstitute/viral-ngs"`
`226`		`- dx_instance_type: "mem1_ssd1_x4"`
	`226`	`+ dx_instance_type: "mem1_ssd1_v2_x4"`
`227`	`227`	`}`
`228`	`228`	`}`
`229`	`229`
`@@ -256,7 +256,7 @@ task aggregate_metagenomics_reports {`
`256`	`256`	`docker: "quay.io/broadinstitute/viral-ngs"`
`257`	`257`	`memory: "4 GB"`
`258`	`258`	`cpu: 1`
`259`		`- dx_instance_type: "mem1_ssd2_x2"`
	`259`	`+ dx_instance_type: "mem1_ssd2_v2_x2"`
`260`	`260`	`preemptible: 0`
`261`	`261`	`}`
`262`	`262`	`}`
Original file line number	Diff line number	Diff line change
`@@ -71,7 +71,7 @@ task deplete_taxa {`
`71`	`71`	`docker: "quay.io/broadinstitute/viral-ngs"`
`72`	`72`	`memory: "14 GB"`
`73`	`73`	`cpu: 8`
`74`		`- dx_instance_type: "mem1_ssd1_x16"`
	`74`	`+ dx_instance_type: "mem1_ssd1_v2_x16"`
`75`	`75`	`preemptible: 0`
`76`	`76`	`}`
`77`	`77`	`}`
`@@ -130,7 +130,7 @@ task filter_to_taxon {`
`130`	`130`	`docker: "quay.io/broadinstitute/viral-ngs"`
`131`	`131`	`memory: "14 GB"`
`132`	`132`	`cpu: 16`
`133`		`- dx_instance_type: "mem1_ssd1_x8"`
	`133`	`+ dx_instance_type: "mem1_ssd1_v2_x8"`
`134`	`134`	`}`
`135`	`135`	`}`
`136`	`136`
`@@ -153,7 +153,7 @@ task build_lastal_db {`
`153`	`153`	`docker: "quay.io/broadinstitute/viral-ngs"`
`154`	`154`	`memory: "7 GB"`
`155`	`155`	`cpu: 2`
`156`		`- dx_instance_type: "mem1_ssd1_x4"`
	`156`	`+ dx_instance_type: "mem1_ssd1_v2_x4"`
`157`	`157`	`}`
`158`	`158`	`}`
`159`	`159`
`@@ -194,7 +194,7 @@ task merge_one_per_sample {`
`194`	`194`	`memory: "7 GB"`
`195`	`195`	`cpu: 4`
`196`	`196`	`docker: "quay.io/broadinstitute/viral-ngs"`
`197`		`- dx_instance_type: "mem1_ssd2_x4"`
	`197`	`+ dx_instance_type: "mem1_ssd1_v2_x16"`
`198`	`198`	`}`
`199`	`199`	`}`
`200`	`200`