Merge pull request #30 from mskcc/feature/increase_core_count

Global increase of core count by 2
mskcc · Jun 18, 2024 · bf6f65c · bf6f65c
2 parents 507efdf + 22fb3ee
commit bf6f65c
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Showing 59 changed files with 59 additions and 59 deletions.
diff --git a/tools/abra/2.17/abra.cwl b/tools/abra/2.17/abra.cwl
@@ -27,7 +27,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: $(inputs.abra_ram_min)
-    coresMin: 16
+    coresMin: 18
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-abra:2.17
 

diff --git a/tools/basic-filtering.complex/0.3/basic-filtering.complex.cwl b/tools/basic-filtering.complex/0.3/basic-filtering.complex.cwl
@@ -13,7 +13,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 2
+    coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-basic-filtering:0.3
 

diff --git a/tools/basic-filtering.mutect/0.3/basic-filtering.mutect.cwl b/tools/basic-filtering.mutect/0.3/basic-filtering.mutect.cwl
@@ -10,7 +10,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 2
+    coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-basic-filtering:0.3
 

diff --git a/tools/basic-filtering.vardict/0.3/basic-filtering.vardict.cwl b/tools/basic-filtering.vardict/0.3/basic-filtering.vardict.cwl
@@ -10,7 +10,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 10000
-    coresMin: 2
+    coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-basic-filtering:0.3
 

diff --git a/tools/bcftools.annotate/1.9/bcftools.annotate.cwl b/tools/bcftools.annotate/1.9/bcftools.annotate.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-htslib:1.9
 

diff --git a/tools/bcftools.concat/1.9/bcftools.concat.cwl b/tools/bcftools.concat/1.9/bcftools.concat.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-htslib:1.9
 

diff --git a/tools/bwa-mem/0.7.12/bwa-mem.cwl b/tools/bwa-mem/0.7.12/bwa-mem.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 32000
-    coresMin: 4
+    coresMin: 6
   DockerRequirement:
     dockerPull: mskcc/bwa_mem:0.7.12
 

diff --git a/tools/bwa-mem/0.7.12/bwa_mem_with_read_groups.cwl b/tools/bwa-mem/0.7.12/bwa_mem_with_read_groups.cwl
@@ -202,7 +202,7 @@ arguments:
 requirements:
   - class: ResourceRequirement
     ramMin: 32000
-    coresMin: 4
+    coresMin: 6
   - class: DockerRequirement
     dockerPull: 'mskcc/bwa_mem:0.7.12'
   - class: InlineJavascriptRequirement

diff --git a/tools/cmo-utils/1.9.15/cmo-fillout.cwl b/tools/cmo-utils/1.9.15/cmo-fillout.cwl
@@ -9,7 +9,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 48000
-    coresMin: 4
+    coresMin: 6
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-cmo-utils:1.9.15
 

diff --git a/tools/cmo-utils/1.9.15/cmo-index.cwl b/tools/cmo-utils/1.9.15/cmo-index.cwl
@@ -8,7 +8,7 @@ label: cmo-index
 requirements:
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-cmo-utils:1.9.15
   InitialWorkDirRequirement:

diff --git a/tools/cmo-utils/1.9.15/cmo-split-reads.cwl b/tools/cmo-utils/1.9.15/cmo-split-reads.cwl
@@ -9,7 +9,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 24000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-cmo-utils:1.9.15
 

diff --git a/tools/conpair/0.3.3/conpair-concordances.cwl b/tools/conpair/0.3.3/conpair-concordances.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-conpair:0.3.3
 

diff --git a/tools/conpair/0.3.3/conpair-contaminations.cwl b/tools/conpair/0.3.3/conpair-contaminations.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-conpair:0.3.3
 

diff --git a/tools/conpair/0.3.3/conpair-pileup.cwl b/tools/conpair/0.3.3/conpair-pileup.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-conpair:0.3.3
 

diff --git a/tools/delly.call/0.7.7/delly.call.cwl b/tools/delly.call/0.7.7/delly.call.cwl
@@ -17,7 +17,7 @@ requirements:
       - $(inputs.tumor_bam)
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-delly:0.7.7
 

diff --git a/tools/delly.filter/0.7.7/delly.filter.cwl b/tools/delly.filter/0.7.7/delly.filter.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-delly:0.7.7
 

diff --git a/tools/delly.merge/0.7.7/delly.merge.cwl b/tools/delly.merge/0.7.7/delly.merge.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-delly:0.7.7
 

diff --git a/tools/disambiguate/1.0.0/disambiguate.cwl b/tools/disambiguate/1.0.0/disambiguate.cwl
@@ -59,7 +59,7 @@ outputs:
 requirements:
   - class: ResourceRequirement
     ramMin: 32000
-    coresMin: 4
+    coresMin: 6
   - class: DockerRequirement
     dockerPull: 'mskcc/disambiguate:1.0.0'
   - class: InlineJavascriptRequirement
diff --git a/tools/facets.doFacets/1.6.3/facets.doFacets.cwl b/tools/facets.doFacets/1.6.3/facets.doFacets.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-facets:1.6.3
 doc: |

diff --git a/tools/gatk.BaseRecalibrator/3.3-0/gatk.BaseRecalibrator.cwl b/tools/gatk.BaseRecalibrator/3.3-0/gatk.BaseRecalibrator.cwl
@@ -33,7 +33,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 24000
-    coresMin: 4
+    coresMin: 6
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-gatk:3.3-0
 

diff --git a/tools/gatk.DepthOfCoverage/3.3-0/gatk.DepthOfCoverage.cwl b/tools/gatk.DepthOfCoverage/3.3-0/gatk.DepthOfCoverage.cwl
@@ -31,7 +31,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-gatk:3.3-0
 

diff --git a/tools/gatk.FindCoveredIntervals/3.3-0/gatk.FindCoveredIntervals.cwl b/tools/gatk.FindCoveredIntervals/3.3-0/gatk.FindCoveredIntervals.cwl
@@ -32,7 +32,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 24000
-    coresMin: 2
+    coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-gatk:3.3-0
 

diff --git a/tools/gatk.PrintReads/3.3-0/gatk.PrintReads.cwl b/tools/gatk.PrintReads/3.3-0/gatk.PrintReads.cwl
@@ -32,7 +32,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 36000
-    coresMin: 2
+    coresMin: 4
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-gatk:3.3-0
 

diff --git a/tools/gatk.mark_duplicates/4.1.0.0/gatk.mark_duplicates.cwl b/tools/gatk.mark_duplicates/4.1.0.0/gatk.mark_duplicates.cwl
@@ -175,7 +175,7 @@ arguments:
 requirements:
   - class: ResourceRequirement
     ramMin: 42000
-    coresMin: 1
+    coresMin: 3
   - class: DockerRequirement
     dockerPull: 'broadinstitute/gatk:4.1.0.0'
   - class: InlineJavascriptRequirement
diff --git a/tools/htstools/0.1.1/snp-pileup.cwl b/tools/htstools/0.1.1/snp-pileup.cwl
@@ -10,7 +10,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-htstools:0.1.1
 

diff --git a/tools/list2bed/1.0.1/list2bed.cwl b/tools/list2bed/1.0.1/list2bed.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 2000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-list2bed:1.0.1
 

diff --git a/tools/mutect/1.1.4/mutect.cwl b/tools/mutect/1.1.4/mutect.cwl
@@ -28,7 +28,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 24000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-mutect:1.1.4
 

diff --git a/tools/ngs-filters/1.4/ngs-filters.cwl b/tools/ngs-filters/1.4/ngs-filters.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 36000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-ngs-filters:1.4
 

diff --git a/tools/picard.AddOrReplaceReadGroups/2.9/picard.AddOrReplaceReadGroups.cwl b/tools/picard.AddOrReplaceReadGroups/2.9/picard.AddOrReplaceReadGroups.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 25000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.CollectAlignmentSummaryMetrics/2.9/picard.CollectAlignmentSummaryMetrics.cwl b/tools/picard.CollectAlignmentSummaryMetrics/2.9/picard.CollectAlignmentSummaryMetrics.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.CollectGcBiasMetrics/2.9/picard.CollectGcBiasMetrics.cwl b/tools/picard.CollectGcBiasMetrics/2.9/picard.CollectGcBiasMetrics.cwl
@@ -35,7 +35,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.CollectHsMetrics/2.9/picard.CollectHsMetrics.cwl b/tools/picard.CollectHsMetrics/2.9/picard.CollectHsMetrics.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.CollectInsertSizeMetrics/2.9/picard.CollectInsertSizeMetrics.cwl b/tools/picard.CollectInsertSizeMetrics/2.9/picard.CollectInsertSizeMetrics.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.CollectMultipleMetrics/2.9/picard.CollectMultipleMetrics.cwl b/tools/picard.CollectMultipleMetrics/2.9/picard.CollectMultipleMetrics.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/picard.MarkDuplicates/2.9/picard.MarkDuplicates.cwl b/tools/picard.MarkDuplicates/2.9/picard.MarkDuplicates.cwl
@@ -34,7 +34,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 42000
-    coresMin: 3
+    coresMin: 5
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-picard:2.9
 

diff --git a/tools/remove-variants/0.1.1/remove-variants.cwl b/tools/remove-variants/0.1.1/remove-variants.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-remove-variants:0.1.1
 

diff --git a/tools/roslin-qc/create-cdna-contam.cwl b/tools/roslin-qc/create-cdna-contam.cwl
@@ -11,7 +11,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/create-hotspots-in-normals.cwl b/tools/roslin-qc/create-hotspots-in-normals.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/create-minor-contam-binlist.cwl b/tools/roslin-qc/create-minor-contam-binlist.cwl
@@ -12,7 +12,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 16000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/generate-cutadapt-summary.cwl b/tools/roslin-qc/generate-cutadapt-summary.cwl
@@ -5,7 +5,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/generate-fingerprint.cwl b/tools/roslin-qc/generate-fingerprint.cwl
@@ -5,7 +5,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/generate-images.cwl b/tools/roslin-qc/generate-images.cwl
@@ -7,7 +7,7 @@ requirements:
     listing: $(inputs.data_dir.listing)
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/generate-qual-files.cwl b/tools/roslin-qc/generate-qual-files.cwl
@@ -5,7 +5,7 @@ requirements:
   InlineJavascriptRequirement: {}
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4
 

diff --git a/tools/roslin-qc/genlatex.cwl b/tools/roslin-qc/genlatex.cwl
@@ -7,7 +7,7 @@ requirements:
     listing: $(inputs.data_dir.listing)
   ResourceRequirement:
     ramMin: 8000
-    coresMin: 1
+    coresMin: 3
   DockerRequirement:
     dockerPull: mskcc/roslin-variant-roslin-qc:0.6.4