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yashpatel6yashpatel6
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Update configtests
1 parent f820dd3 commit 0df06d3

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Lines changed: 84 additions & 2 deletions

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‎test/configtest-F16.json‎

Lines changed: 42 additions & 1 deletion
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@@ -67,6 +67,10 @@
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"cpus": "6",
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"memory": "6 GB"
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},
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"call_sSNV_DeepSomatic": {
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"cpus": "4",
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"memory": "15 GB"
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},
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"call_sSNV_MuSE": {
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"cpus": "6",
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"memory": "24 GB"
@@ -91,6 +95,10 @@
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"cpus": "1",
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"memory": "1 GB"
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},
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"convert_IntervalListToBed_GATK": {
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"cpus": "1",
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"memory": "1 GB"
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},
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"create_IndelCandidate_SAMtools": {
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"cpus": "1",
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"memory": "1 GB"
@@ -122,12 +130,14 @@
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"call_ssnv_r_version": "dev",
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"dataset_id": "TWGSAMIN",
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"dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz",
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"deepsomatic_version": "1.9.0",
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"docker_container_registry": "ghcr.io/uclahs-cds",
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"docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21",
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"docker_image_GATK": "broadinstitute/gatk:4.6.1.0",
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"docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.1.2",
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"docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam_readcount:1.0.1",
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"docker_image_bpg": "ghcr.io/uclahs-cds/boutroslabplottinggeneral:7.1.0",
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"docker_image_deepsomatic": "google/deepsomatic:1.9.0",
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"docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0",
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"docker_image_r_VennDiagram": "ghcr.io/uclahs-cds/call-ssnv-r:dev",
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"docker_image_somaticsniper": "ghcr.io/uclahs-cds/somaticsniper:1.0.5.0",
@@ -183,6 +193,12 @@
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"strategy": "add"
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}
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},
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"call_sSNV_DeepSomatic": {
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"memory": {
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"operand": "10 GB",
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"strategy": "add"
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}
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},
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"call_sSNV_MuSE": {
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"memory": {
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"operand": "8 GB",
@@ -219,6 +235,12 @@
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"strategy": "add"
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}
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},
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"convert_IntervalListToBed_GATK": {
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"memory": {
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"operand": "2",
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"strategy": "exponential"
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}
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},
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"create_IndelCandidate_SAMtools": {
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"memory": {
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"operand": "5 GB",
@@ -374,6 +396,15 @@
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"cpus": "6",
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"memory": "6 GB"
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},
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"withName:call_sSNV_DeepSomatic": {
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"cpus": "4",
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"memory": {
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"1": "15 GB",
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"2": "25 GB",
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"3": "31 GB",
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"closure": "retry_updater(15 GB, add, 10 GB, $task.attempt, memory)"
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}
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},
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"withName:call_sSNV_MuSE": {
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"cpus": "6",
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"memory": {
@@ -431,6 +462,15 @@
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"closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
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}
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},
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"withName:convert_IntervalListToBed_GATK": {
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"cpus": "1",
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"memory": {
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"1": "1 GB",
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"2": "2 GB",
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"3": "4 GB",
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"closure": "retry_updater(1 GB, exponential, 2, $task.attempt, memory)"
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}
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},
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"withName:create_IndelCandidate_SAMtools": {
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"cpus": "1",
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"memory": {
@@ -504,7 +544,8 @@
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"somaticsniper",
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"strelka2",
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"mutect2",
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"muse"
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"muse",
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"deepsomatic"
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],
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"workDir": "/scratch/8543"
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}

‎test/configtest-F32.json‎

Lines changed: 42 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -67,6 +67,10 @@
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"cpus": "8",
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"memory": "6 GB"
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},
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"call_sSNV_DeepSomatic": {
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"cpus": "4",
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"memory": "20 GB"
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},
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"call_sSNV_MuSE": {
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"cpus": "12",
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"memory": "48 GB"
@@ -91,6 +95,10 @@
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"cpus": "1",
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"memory": "1 GB"
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},
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"convert_IntervalListToBed_GATK": {
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"cpus": "1",
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"memory": "1 GB"
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},
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"create_IndelCandidate_SAMtools": {
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"cpus": "1",
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"memory": "1 GB"
@@ -122,12 +130,14 @@
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"call_ssnv_r_version": "dev",
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"dataset_id": "TWGSAMIN",
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"dbSNP": "/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz",
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"deepsomatic_version": "1.9.0",
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"docker_container_registry": "ghcr.io/uclahs-cds",
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"docker_image_BCFtools": "ghcr.io/uclahs-cds/bcftools:1.21",
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"docker_image_GATK": "broadinstitute/gatk:4.6.1.0",
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"docker_image_MuSE": "ghcr.io/uclahs-cds/muse:2.1.2",
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"docker_image_bam_readcount": "ghcr.io/uclahs-cds/bam_readcount:1.0.1",
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"docker_image_bpg": "ghcr.io/uclahs-cds/boutroslabplottinggeneral:7.1.0",
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"docker_image_deepsomatic": "google/deepsomatic:1.9.0",
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"docker_image_manta": "ghcr.io/uclahs-cds/manta:1.6.0",
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"docker_image_r_VennDiagram": "ghcr.io/uclahs-cds/call-ssnv-r:dev",
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"docker_image_somaticsniper": "ghcr.io/uclahs-cds/somaticsniper:1.0.5.0",
@@ -183,6 +193,12 @@
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"strategy": "add"
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}
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},
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"call_sSNV_DeepSomatic": {
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"memory": {
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"operand": "10 GB",
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"strategy": "add"
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}
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},
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"call_sSNV_MuSE": {
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"memory": {
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"operand": "16 GB",
@@ -219,6 +235,12 @@
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"strategy": "add"
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}
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},
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"convert_IntervalListToBed_GATK": {
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"memory": {
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"operand": "2",
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"strategy": "exponential"
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}
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},
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"create_IndelCandidate_SAMtools": {
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"memory": {
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"operand": "5 GB",
@@ -374,6 +396,15 @@
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"cpus": "8",
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"memory": "6 GB"
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},
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"withName:call_sSNV_DeepSomatic": {
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"cpus": "4",
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"memory": {
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"1": "20 GB",
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"2": "30 GB",
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"3": "40 GB",
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"closure": "retry_updater(20 GB, add, 10 GB, $task.attempt, memory)"
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}
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},
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"withName:call_sSNV_MuSE": {
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"cpus": "12",
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"memory": {
@@ -431,6 +462,15 @@
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"closure": "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
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}
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},
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"withName:convert_IntervalListToBed_GATK": {
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"cpus": "1",
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"memory": {
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"1": "1 GB",
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"2": "2 GB",
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"3": "4 GB",
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"closure": "retry_updater(1 GB, exponential, 2, $task.attempt, memory)"
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}
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},
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"withName:create_IndelCandidate_SAMtools": {
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"cpus": "1",
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"memory": {
@@ -504,7 +544,8 @@
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"somaticsniper",
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"strelka2",
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"mutect2",
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"muse"
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"muse",
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"deepsomatic"
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],
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"workDir": "/scratch/8543"
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}

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