diff --git a/tools/abra/2.17/abra.cwl b/tools/abra/2.17/abra.cwl index 315084a..caa30e2 100644 --- 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 index 9b2818c..a62d347 100644 --- 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 index 609ce03..49df127 100644 --- 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 index 20ad57d..00035e0 100644 --- 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 index d1a6071..988242b 100644 --- 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 index 31ecb18..cfd6db7 100644 --- 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 index 423454b..7c58c45 100644 --- 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 index 365762e..3215f3a 100644 --- 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 index ffc521b..92ab3bd 100644 --- 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 index b035894..3abd2f8 100644 --- 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 index 0cfe0d2..a920b4b 100644 --- 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 index e09c142..d88bfea 100644 --- 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 index a08add0..48f9dca 100644 --- 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 index 8bb7039..e583940 100644 --- 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 index 3d7241a..c15a6a1 100644 --- 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 index d254e9d..64123d9 100644 --- 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 index eba8120..650bf95 100644 --- 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 index f5d5f7f..6db5524 100644 --- 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 index 6690377..a6bcd32 100644 --- 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 index afc90e5..2da87ff 100644 --- 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 index 4b31475..c7810cf 100644 --- 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 index 0e63673..cf317ce 100644 --- 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 index 635f9b1..241dd3b 100644 --- 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 index 2b92a23..832a010 100644 --- 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 index 883714b..0a71e17 100644 --- 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 index edd0de2..3f8048a 100644 --- 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 index d2c9496..bfdb18e 100644 --- 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 index 7d233c1..623732b 100644 --- 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 index 0df24e8..b5dfc6a 100644 --- 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 index 0cd4b5a..9f88331 100644 --- 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 index 20ef35e..cd23739 100644 --- 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 index 56baa4b..5125f5e 100644 --- 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 index a529396..c4a6806 100644 --- 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 index 1da5e4b..80b008f 100644 --- 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 index 29a6fcc..36cc5ad 100644 --- 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 index f335fe5..3e0bd07 100644 --- 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 index 25872c5..3095a01 100644 --- 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 index b7cf59e..284b05f 100644 --- 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 index 62587f9..98830e2 100644 --- 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 index e84ef87..1bebd36 100644 --- 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 index 1b5c4f7..3716dae 100644 --- 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 index b35a905..f636de3 100644 --- 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 index 5df3bc8..9ba1b4a 100644 --- 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 index e7ca46d..879b880 100644 --- 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 diff --git a/tools/roslin-qc/merge-gcbias-metrics.cwl b/tools/roslin-qc/merge-gcbias-metrics.cwl index c157dd2..6b5d737 100644 --- a/tools/roslin-qc/merge-gcbias-metrics.cwl +++ b/tools/roslin-qc/merge-gcbias-metrics.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/merge-insert-size-histograms.cwl b/tools/roslin-qc/merge-insert-size-histograms.cwl index 5f6fa14..7554128 100644 --- a/tools/roslin-qc/merge-insert-size-histograms.cwl +++ b/tools/roslin-qc/merge-insert-size-histograms.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/merge-picard-metrics-hsmetrics.cwl b/tools/roslin-qc/merge-picard-metrics-hsmetrics.cwl index e890cfa..3a9dd20 100644 --- a/tools/roslin-qc/merge-picard-metrics-hsmetrics.cwl +++ b/tools/roslin-qc/merge-picard-metrics-hsmetrics.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/merge-picard-metrics-markduplicates.cwl b/tools/roslin-qc/merge-picard-metrics-markduplicates.cwl index d661823..e4a5973 100644 --- a/tools/roslin-qc/merge-picard-metrics-markduplicates.cwl +++ b/tools/roslin-qc/merge-picard-metrics-markduplicates.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/stitch-pdf.cwl b/tools/roslin-qc/stitch-pdf.cwl index b724467..644889c 100644 --- a/tools/roslin-qc/stitch-pdf.cwl +++ b/tools/roslin-qc/stitch-pdf.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/samtools.merge/1.9/samtools.merge.cwl b/tools/samtools.merge/1.9/samtools.merge.cwl index 5746b36..707e9d7 100644 --- a/tools/samtools.merge/1.9/samtools.merge.cwl +++ b/tools/samtools.merge/1.9/samtools.merge.cwl @@ -23,7 +23,7 @@ arguments: requirements: - class: ResourceRequirement ramMin: 32000 - coresMin: 4 + coresMin: 6 - class: DockerRequirement dockerPull: 'mjblow/samtools-1.9:latest' - class: InlineJavascriptRequirement diff --git a/tools/samtools.sort/1.3.1/samtools.sort.cwl b/tools/samtools.sort/1.3.1/samtools.sort.cwl index e958efd..d0a4196 100644 --- a/tools/samtools.sort/1.3.1/samtools.sort.cwl +++ b/tools/samtools.sort/1.3.1/samtools.sort.cwl @@ -116,7 +116,7 @@ arguments: requirements: - class: ResourceRequirement ramMin: 32000 - coresMin: 4 + coresMin: 6 - class: DockerRequirement dockerPull: mskcc/roslin-variant-samtools:1.3.1 - class: InlineJavascriptRequirement \ No newline at end of file diff --git a/tools/samtools.view/1.3.1/samtools.view.cwl b/tools/samtools.view/1.3.1/samtools.view.cwl index fb31463..2b496ca 100644 --- a/tools/samtools.view/1.3.1/samtools.view.cwl +++ b/tools/samtools.view/1.3.1/samtools.view.cwl @@ -418,7 +418,7 @@ arguments: requirements: - class: ResourceRequirement ramMin: 32000 - coresMin: 4 + coresMin: 6 - class: DockerRequirement dockerPull: mskcc/roslin-variant-samtools:1.3.1 - class: InlineJavascriptRequirement diff --git a/tools/tabix/1.9/tabix.cwl b/tools/tabix/1.9/tabix.cwl index b375ccc..b822b9e 100644 --- a/tools/tabix/1.9/tabix.cwl +++ b/tools/tabix/1.9/tabix.cwl @@ -11,7 +11,7 @@ requirements: listing: [ $(inputs.input_vcf) ] ResourceRequirement: ramMin: 80000 - coresMin: 1 + coresMin: 3 DockerRequirement: dockerPull: mskcc/roslin-variant-htslib:1.9 diff --git a/tools/trimgalore/0.2.5.mod/trimgalore.cwl b/tools/trimgalore/0.2.5.mod/trimgalore.cwl index b70b68c..3417c4d 100644 --- a/tools/trimgalore/0.2.5.mod/trimgalore.cwl +++ b/tools/trimgalore/0.2.5.mod/trimgalore.cwl @@ -10,7 +10,7 @@ requirements: - var getBaseName = function(inputFile) { return inputFile.basename; }; - class: ResourceRequirement ramMin: 12000 - coresMin: 1 + coresMin: 3 - class: DockerRequirement dockerPull: mskcc/roslin-variant-trimgalore:0.2.5.mod diff --git a/tools/unpack-bam/0.1.0/unpack-bam.cwl b/tools/unpack-bam/0.1.0/unpack-bam.cwl index c548608..3605bfb 100644 --- a/tools/unpack-bam/0.1.0/unpack-bam.cwl +++ b/tools/unpack-bam/0.1.0/unpack-bam.cwl @@ -24,7 +24,7 @@ requirements: InlineJavascriptRequirement: {} ResourceRequirement: ramMin: 16000 - coresMin: 2 + coresMin: 4 inputs: - id: input_bam diff --git a/tools/vardict/1.5.1/testsomatic.cwl b/tools/vardict/1.5.1/testsomatic.cwl index 02b00c0..48b330b 100644 --- a/tools/vardict/1.5.1/testsomatic.cwl +++ b/tools/vardict/1.5.1/testsomatic.cwl @@ -9,7 +9,7 @@ id: testsomatic requirements: InlineJavascriptRequirement: {} ResourceRequirement: - coresMin: 2 + coresMin: 4 ramMin: 12000 DockerRequirement: dockerPull: mskcc/roslin-variant-vardict:1.5.1 diff --git a/tools/vardict/1.5.1/var_to_vcf.cwl b/tools/vardict/1.5.1/var_to_vcf.cwl index 670fcfc..d3829ce 100644 --- a/tools/vardict/1.5.1/var_to_vcf.cwl +++ b/tools/vardict/1.5.1/var_to_vcf.cwl @@ -14,7 +14,7 @@ arguments: requirements: InlineJavascriptRequirement: {} ResourceRequirement: - coresMin: 4 + coresMin: 6 ramMin: 32000 DockerRequirement: dockerPull: mskcc/roslin-variant-vardict:1.5.1 diff --git a/tools/vardict/1.5.1/vardict_app.cwl b/tools/vardict/1.5.1/vardict_app.cwl index 9035588..5a93013 100644 --- a/tools/vardict/1.5.1/vardict_app.cwl +++ b/tools/vardict/1.5.1/vardict_app.cwl @@ -18,7 +18,7 @@ arguments: requirements: InlineJavascriptRequirement: {} ResourceRequirement: - coresMin: 4 + coresMin: 6 ramMin: 24000 DockerRequirement: dockerPull: mskcc/roslin-variant-vardict:1.5.1 diff --git a/tools/vcf2maf/1.6.17/vcf2maf.cwl b/tools/vcf2maf/1.6.17/vcf2maf.cwl index 8c41ad1..301cada 100644 --- a/tools/vcf2maf/1.6.17/vcf2maf.cwl +++ b/tools/vcf2maf/1.6.17/vcf2maf.cwl @@ -17,7 +17,7 @@ requirements: InlineJavascriptRequirement: {} ResourceRequirement: ramMin: 8000 - coresMin: 2 + coresMin: 4 DockerRequirement: dockerPull: mskcc/roslin-variant-vcf2maf:1.6.17