➕ update picard tools to use 2.18.9R docker

kids-first · Jun 3, 2021 · 579aab3 · 579aab3
1 parent c16b51b
commit 579aab3
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Showing 29 changed files with 29 additions and 29 deletions.
diff --git a/tools/picard_calculatereadgroupchecksum.cwl b/tools/picard_calculatereadgroupchecksum.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 4000
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, CalculateReadGroupChecksum]

diff --git a/tools/picard_checkfingerprint.cwl b/tools/picard_checkfingerprint.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms2000m, -Xmx8000m, -jar, /picard.jar, CheckFingerprint]

diff --git a/tools/picard_collectaggregationmetrics.cwl b/tools/picard_collectaggregationmetrics.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 12000
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectMultipleMetrics]

diff --git a/tools/picard_collectaggregationmetrics_conditional.cwl b/tools/picard_collectaggregationmetrics_conditional.cwl
@@ -11,7 +11,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 12000
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectMultipleMetrics]

diff --git a/tools/picard_collectalignmentsummarymetrics_conditional.cwl b/tools/picard_collectalignmentsummarymetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 12000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectAlignmentSummaryMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectgcbiasmetrics_conditional.cwl b/tools/picard_collectgcbiasmetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 12000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectGcBiasMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectgvcfcallingmetrics.cwl b/tools/picard_collectgvcfcallingmetrics.cwl
@@ -12,7 +12,7 @@ requirements:
     ramMin: 3000
     coresMin: 16
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [java, -Xms2000m, -jar, /picard.jar, CollectVariantCallingMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collecthsmetrics.cwl b/tools/picard_collecthsmetrics.cwl
@@ -7,7 +7,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 8000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, CollectHsMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collecthsmetrics_conditional.cwl b/tools/picard_collecthsmetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 8000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, CollectHsMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectinsertsizemetrics_conditional.cwl b/tools/picard_collectinsertsizemetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 12000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectInsertSizeMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectqualityyieldmetrics.cwl b/tools/picard_collectqualityyieldmetrics.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, CollectQualityYieldMetrics]

diff --git a/tools/picard_collectrawwgsmetrics.cwl b/tools/picard_collectrawwgsmetrics.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms2000m, -Xmx8000m, -jar, /picard.jar, CollectRawWgsMetrics]

diff --git a/tools/picard_collectreadgroupbamqualitymetrics.cwl b/tools/picard_collectreadgroupbamqualitymetrics.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectMultipleMetrics]

diff --git a/tools/picard_collectsequencingartifactmetrics_conditional.cwl b/tools/picard_collectsequencingartifactmetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 12000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectSequencingArtifactMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectunsortedreadgroupbamqualitymetrics.cwl b/tools/picard_collectunsortedreadgroupbamqualitymetrics.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, CollectMultipleMetrics]

diff --git a/tools/picard_collectwgsmetrics.cwl b/tools/picard_collectwgsmetrics.cwl
@@ -7,7 +7,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 8000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, CollectWgsMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_collectwgsmetrics_conditional.cwl b/tools/picard_collectwgsmetrics_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 8000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms2000m, -Xmx6000m, -XX:GCTimeLimit=50, -XX:GCHeapFreeLimit=10, -jar, /picard.jar, CollectWgsMetrics]
 arguments:
   - position: 1

diff --git a/tools/picard_gatherbamfiles.cwl b/tools/picard_gatherbamfiles.cwl
@@ -10,7 +10,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: []

diff --git a/tools/picard_intervallisttools.cwl b/tools/picard_intervallisttools.cwl
@@ -9,7 +9,7 @@ requirements:
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [java, -Xmx2000m, -jar, /picard.jar]
 arguments:
   - position: 1

diff --git a/tools/picard_markduplicates.cwl b/tools/picard_markduplicates.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 id: picard_markduplicates
 requirements:
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement

diff --git a/tools/picard_markduplicates_single.cwl b/tools/picard_markduplicates_single.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 id: picard_markduplicates_single
 requirements:
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement

diff --git a/tools/picard_mergevcfs.cwl b/tools/picard_mergevcfs.cwl
@@ -11,7 +11,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 3000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms2000m, -jar, /picard.jar, MergeVcfs]
 arguments:
   - position: 1

diff --git a/tools/picard_mergevcfs_python_renamesample.cwl b/tools/picard_mergevcfs_python_renamesample.cwl
@@ -7,7 +7,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 3000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: ["/bin/bash", "-c"]
 arguments:
   - position: 1

diff --git a/tools/picard_qualityscoredistribution_conditional.cwl b/tools/picard_qualityscoredistribution_conditional.cwl
@@ -13,7 +13,7 @@ requirements:
   - class: ResourceRequirement
     ramMin: 12000
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard-r:latest-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [ java, -Xms5000m, -jar, /picard.jar, QualityScoreDistribution]
 arguments:
   - position: 1

diff --git a/tools/picard_renamesample.cwl b/tools/picard_renamesample.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
 baseCommand: [java, -Xmx2000m, -jar, /picard.jar]
 arguments:
   - position: 1

diff --git a/tools/picard_revertsam.cwl b/tools/picard_revertsam.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 id: picard_revertsam
 requirements:
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ShellCommandRequirement
 baseCommand: [java, -Xms8000m, -jar, /picard.jar]
 arguments:

diff --git a/tools/picard_samtofastq.cwl b/tools/picard_samtofastq.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 id: picard_samtofastq
 requirements:
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ShellCommandRequirement
   - class: InlineJavascriptRequirement
   - class: ResourceRequirement

diff --git a/tools/picard_sortsam.cwl b/tools/picard_sortsam.cwl
@@ -3,7 +3,7 @@ class: CommandLineTool
 id: picard_sortsam
 requirements:
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ShellCommandRequirement
   - class: ResourceRequirement
     ramMin: 8000

diff --git a/tools/picard_validatesamfile.cwl b/tools/picard_validatesamfile.cwl
@@ -5,7 +5,7 @@ requirements:
   - class: InlineJavascriptRequirement
   - class: ShellCommandRequirement
   - class: DockerRequirement
-    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.2-dev'
+    dockerPull: 'pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R'
   - class: ResourceRequirement
     ramMin: 8000
 baseCommand: [ java, -Xms2000m, -Xmx8000m, -jar, /picard.jar, ValidateSamFile]