concat.threads |
Int |
4 |
Number of threads to request |
concat.jobMemory |
Int |
16 |
Memory allocated for this job |
concat.timeout |
Int |
72 |
Hours before task timeout |
concat.modules |
String |
"tabix/0.2.6" |
Required environment modules |
align.modules |
String |
"consensus-cruncher/5.0 data-hg19-consensus-cruncher/1.0 hg19-bwa-index/0.7.12 samtools/1.9" |
Names and versions of modules to load |
align.consensusCruncherPy |
String |
"$CONSENSUS_CRUNCHER_ROOT/bin/ConsensusCruncher.py" |
Path to consensusCruncher binary |
align.bwa |
String |
"$BWA_ROOT/bin/bwa" |
Path to bwa binary |
align.bwaref |
String |
"$HG19_BWA_INDEX_ROOT/hg19_random.fa" |
Path to bwa index |
align.samtools |
String |
"$SAMTOOLS_ROOT/bin/samtools" |
Path to samtools binary |
align.blist |
String |
"$DATA_HG19_CONSENSUS_CRUNCHER_ROOT/IDT_duplex_sequencing_barcodes.list" |
Path to blacklist for barcodes |
align.threads |
Int |
4 |
Number of threads to request |
align.jobMemory |
Int |
16 |
Memory allocated for this job |
align.timeout |
Int |
72 |
Hours before task timeout |
consensus.consensusCruncherPy |
String |
"$CONSENSUS_CRUNCHER_ROOT/bin/ConsensusCruncher.py" |
Path to consensusCruncher binary |
consensus.samtools |
String |
"$SAMTOOLS_ROOT/bin/samtools" |
Path to samtools binary |
consensus.cytoband |
String |
"$DATA_HG19_CONSENSUS_CRUNCHER_ROOT/hg19_cytoBand.txt" |
Path to cytoband for genome |
consensus.genome |
String |
"hg19" |
Which genome version to use |
consensus.ccDir |
String |
basePrefix + ".consensuscruncher" |
Placeholder |
consensus.cutoff |
Float |
0.7 |
Cutoff to use to call a consenus of reads |
consensus.threads |
Int |
8 |
Number of threads to request |
consensus.jobMemory |
Int |
32 |
Memory allocated for this job |
consensus.timeout |
Int |
72 |
Hours before task timeout |
consensus.modules |
String |
"consensus-cruncher/5.0 data-hg19-consensus-cruncher/1.0 hg19-bwa-index/0.7.12 samtools/1.9" |
Names and versions of modules to load |
mutectRunDCSSC.filter_timeout |
Int |
12 |
- |
mutectRunDCSSC.filter_memory |
Int |
16 |
- |
mutectRunDCSSC.filter_filterExtraArgs |
String? |
None |
- |
mutectRunDCSSC.mergeStats_timeout |
Int |
5 |
- |
mutectRunDCSSC.mergeStats_memory |
Int |
4 |
- |
mutectRunDCSSC.mergeStats_modules |
String |
"gatk/4.1.6.0" |
- |
mutectRunDCSSC.mergeVCFs_timeout |
Int |
12 |
Hours before task timeout |
mutectRunDCSSC.mergeVCFs_memory |
Int |
4 |
Memory allocated for job |
mutectRunDCSSC.runMutect2_timeout |
Int |
24 |
- |
mutectRunDCSSC.runMutect2_memory |
Int |
32 |
- |
mutectRunDCSSC.runMutect2_threads |
Int |
4 |
- |
mutectRunDCSSC.runMutect2_mutect2ExtraArgs |
String? |
None |
- |
mutectRunDCSSC.runMutect2_mutectTag |
String |
"mutect2" |
- |
mutectRunDCSSC.splitStringToArray_modules |
String |
"" |
- |
mutectRunDCSSC.splitStringToArray_timeout |
Int |
1 |
- |
mutectRunDCSSC.splitStringToArray_memory |
Int |
1 |
- |
mutectRunDCSSC.splitStringToArray_lineSeparator |
String |
"," |
- |
mutectRunDCSSC.normalBam |
File? |
None |
Input normal file (bam or sam). |
mutectRunDCSSC.normalBai |
File? |
None |
- |
mutectRunDCSSC.pon |
File? |
None |
- |
mutectRunDCSSC.ponIdx |
File? |
None |
- |
mutectRunDCSSC.gnomad |
File? |
None |
- |
mutectRunDCSSC.gnomadIdx |
File? |
None |
- |
mutectRunSSCSSC.filter_timeout |
Int |
12 |
- |
mutectRunSSCSSC.filter_memory |
Int |
16 |
- |
mutectRunSSCSSC.filter_filterExtraArgs |
String? |
None |
- |
mutectRunSSCSSC.mergeStats_timeout |
Int |
5 |
- |
mutectRunSSCSSC.mergeStats_memory |
Int |
4 |
- |
mutectRunSSCSSC.mergeStats_modules |
String |
"gatk/4.1.6.0" |
- |
mutectRunSSCSSC.mergeVCFs_timeout |
Int |
12 |
Hours before task timeout |
mutectRunSSCSSC.mergeVCFs_memory |
Int |
4 |
Memory allocated for job |
mutectRunSSCSSC.runMutect2_timeout |
Int |
24 |
- |
mutectRunSSCSSC.runMutect2_memory |
Int |
32 |
- |
mutectRunSSCSSC.runMutect2_threads |
Int |
4 |
- |
mutectRunSSCSSC.runMutect2_mutect2ExtraArgs |
String? |
None |
- |
mutectRunSSCSSC.runMutect2_mutectTag |
String |
"mutect2" |
- |
mutectRunSSCSSC.splitStringToArray_modules |
String |
"" |
- |
mutectRunSSCSSC.splitStringToArray_timeout |
Int |
1 |
- |
mutectRunSSCSSC.splitStringToArray_memory |
Int |
1 |
- |
mutectRunSSCSSC.splitStringToArray_lineSeparator |
String |
"," |
- |
mutectRunSSCSSC.normalBam |
File? |
None |
Input normal file (bam or sam). |
mutectRunSSCSSC.normalBai |
File? |
None |
- |
mutectRunSSCSSC.pon |
File? |
None |
- |
mutectRunSSCSSC.ponIdx |
File? |
None |
- |
mutectRunSSCSSC.gnomad |
File? |
None |
- |
mutectRunSSCSSC.gnomadIdx |
File? |
None |
- |
mutectRunAllUnique.filter_timeout |
Int |
12 |
- |
mutectRunAllUnique.filter_memory |
Int |
16 |
- |
mutectRunAllUnique.filter_filterExtraArgs |
String? |
None |
- |
mutectRunAllUnique.mergeStats_timeout |
Int |
5 |
- |
mutectRunAllUnique.mergeStats_memory |
Int |
4 |
- |
mutectRunAllUnique.mergeStats_modules |
String |
"gatk/4.1.6.0" |
- |
mutectRunAllUnique.mergeVCFs_timeout |
Int |
12 |
Hours before task timeout |
mutectRunAllUnique.mergeVCFs_memory |
Int |
4 |
Memory allocated for job |
mutectRunAllUnique.runMutect2_timeout |
Int |
24 |
- |
mutectRunAllUnique.runMutect2_memory |
Int |
32 |
- |
mutectRunAllUnique.runMutect2_threads |
Int |
4 |
- |
mutectRunAllUnique.runMutect2_mutect2ExtraArgs |
String? |
None |
- |
mutectRunAllUnique.runMutect2_mutectTag |
String |
"mutect2" |
- |
mutectRunAllUnique.splitStringToArray_modules |
String |
"" |
- |
mutectRunAllUnique.splitStringToArray_timeout |
Int |
1 |
- |
mutectRunAllUnique.splitStringToArray_memory |
Int |
1 |
- |
mutectRunAllUnique.splitStringToArray_lineSeparator |
String |
"," |
- |
mutectRunAllUnique.normalBam |
File? |
None |
Input normal file (bam or sam). |
mutectRunAllUnique.normalBai |
File? |
None |
- |
mutectRunAllUnique.pon |
File? |
None |
- |
mutectRunAllUnique.ponIdx |
File? |
None |
- |
mutectRunAllUnique.gnomad |
File? |
None |
- |
mutectRunAllUnique.gnomadIdx |
File? |
None |
- |
hsMetricsRunDCSSC.collectHSmetrics_timeout |
Int |
5 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunDCSSC.collectHSmetrics_maxRecordsInRam |
Int |
250000 |
Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed. |
hsMetricsRunDCSSC.collectHSmetrics_coverageCap |
Int |
500 |
Parameter to set a max coverage limit for Theoretical Sensitivity calculations |
hsMetricsRunDCSSC.collectHSmetrics_jobMemory |
Int |
18 |
Memory allocated to job |
hsMetricsRunDCSSC.collectHSmetrics_filter |
String |
"LENIENT" |
Settings for picard filter |
hsMetricsRunDCSSC.collectHSmetrics_metricTag |
String |
"HS" |
Extension for metrics file |
hsMetricsRunDCSSC.bedToBaitIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunDCSSC.bedToBaitIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
hsMetricsRunDCSSC.bedToTargetIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunDCSSC.bedToTargetIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
hsMetricsRunSSCSSC.collectHSmetrics_timeout |
Int |
5 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunSSCSSC.collectHSmetrics_maxRecordsInRam |
Int |
250000 |
Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed. |
hsMetricsRunSSCSSC.collectHSmetrics_coverageCap |
Int |
500 |
Parameter to set a max coverage limit for Theoretical Sensitivity calculations |
hsMetricsRunSSCSSC.collectHSmetrics_jobMemory |
Int |
18 |
Memory allocated to job |
hsMetricsRunSSCSSC.collectHSmetrics_filter |
String |
"LENIENT" |
Settings for picard filter |
hsMetricsRunSSCSSC.collectHSmetrics_metricTag |
String |
"HS" |
Extension for metrics file |
hsMetricsRunSSCSSC.bedToBaitIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunSSCSSC.bedToBaitIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
hsMetricsRunSSCSSC.bedToTargetIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunSSCSSC.bedToTargetIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
hsMetricsRunAllUnique.collectHSmetrics_timeout |
Int |
5 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunAllUnique.collectHSmetrics_maxRecordsInRam |
Int |
250000 |
Specifies the N of records stored in RAM before spilling to disk. Increasing this number increases the amount of RAM needed. |
hsMetricsRunAllUnique.collectHSmetrics_coverageCap |
Int |
500 |
Parameter to set a max coverage limit for Theoretical Sensitivity calculations |
hsMetricsRunAllUnique.collectHSmetrics_jobMemory |
Int |
18 |
Memory allocated to job |
hsMetricsRunAllUnique.collectHSmetrics_filter |
String |
"LENIENT" |
Settings for picard filter |
hsMetricsRunAllUnique.collectHSmetrics_metricTag |
String |
"HS" |
Extension for metrics file |
hsMetricsRunAllUnique.bedToBaitIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunAllUnique.bedToBaitIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
hsMetricsRunAllUnique.bedToTargetIntervals_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
hsMetricsRunAllUnique.bedToTargetIntervals_jobMemory |
Int |
16 |
Memory allocated to job |
combineVariants.jobMemory |
Int |
24 |
memory allocated to preprocessing, in GB |
combineVariants.timeout |
Int |
20 |
timeout in hours |
combineVariants.threads |
Int |
8 |
number of cpu threads to be used |
annotation.modules |
String |
"samtools/1.9 bcftools/1.9 htslib/1.9 tabix/1.9" |
module for running preprocessing |
annotation.jobMemory |
Int |
24 |
memory allocated to preprocessing, in GB |
annotation.timeout |
Int |
20 |
timeout in hours |
annotation.threads |
Int |
8 |
number of cpu threads to be used |
variantEffectPredictor.mergeVcfs_timeout |
Int |
24 |
Maximum amount of time (in hours) the task can run for. |
variantEffectPredictor.mergeVcfs_threads |
Int |
4 |
Requested CPU threads. |
variantEffectPredictor.mergeVcfs_overhead |
Int |
6 |
Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory. |
variantEffectPredictor.mergeVcfs_jobMemory |
Int |
24 |
Memory allocated to job (in GB). |
variantEffectPredictor.mergeVcfs_extraArgs |
String? |
None |
Additional arguments to be passed directly to the command. |
variantEffectPredictor.mergeVcfs_modules |
String |
"gatk/4.1.7.0" |
Required environment modules. |
variantEffectPredictor.mergeMafs_timeout |
Int |
24 |
Maximum amount of time (in hours) the task can run for. |
variantEffectPredictor.mergeMafs_threads |
Int |
4 |
Requested CPU threads. |
variantEffectPredictor.mergeMafs_jobMemory |
Int |
24 |
Memory allocated to job (in GB). |
variantEffectPredictor.mergeMafs_modules |
String |
"tabix/0.2.6" |
Required environment modules |
variantEffectPredictor.vcf2maf_timeout |
Int |
48 |
Hours before task timeout |
variantEffectPredictor.vcf2maf_threads |
Int |
4 |
Requested CPU threads |
variantEffectPredictor.vcf2maf_jobMemory |
Int |
32 |
Memory allocated for this job (GB) |
variantEffectPredictor.vcf2maf_bufferSize |
Int |
200 |
The buffer size |
variantEffectPredictor.vcf2maf_minHomVaf |
Float |
0.7 |
The minimum vaf for homozygous calls |
variantEffectPredictor.vcf2maf_maxfilterAC |
Int |
10 |
The maximum AC filter |
variantEffectPredictor.vcf2maf_species |
String |
"homo_sapiens" |
Species name |
variantEffectPredictor.vcf2maf_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |
variantEffectPredictor.tumorOnlyAlign_timeout |
Int |
6 |
Hours before task timeout |
variantEffectPredictor.tumorOnlyAlign_threads |
Int |
4 |
Requested CPU threads |
variantEffectPredictor.tumorOnlyAlign_jobMemory |
Int |
32 |
Memory allocated for this job (GB) |
variantEffectPredictor.tumorOnlyAlign_modules |
String |
"bcftools/1.9 tabix/0.2.6" |
Required environment modules |
variantEffectPredictor.tumorOnlyAlign_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |
variantEffectPredictor.vep_timeout |
Int |
16 |
Hours before task timeout |
variantEffectPredictor.vep_threads |
Int |
4 |
Requested CPU threads |
variantEffectPredictor.vep_jobMemory |
Int |
32 |
Memory allocated for this job (GB) |
variantEffectPredictor.vep_species |
String |
"homo_sapiens" |
Species name |
variantEffectPredictor.vep_addParam |
String? |
None |
Additional vep parameters |
variantEffectPredictor.vep_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |
variantEffectPredictor.subsetVcf_timeout |
Int |
6 |
Maximum amount of time (in hours) the task can run for. |
variantEffectPredictor.subsetVcf_threads |
Int |
4 |
Requested CPU threads. |
variantEffectPredictor.subsetVcf_jobMemory |
Int |
32 |
Memory allocated to job (in GB). |
variantEffectPredictor.subsetVcf_modules |
String |
"bcftools/1.9" |
Required environment modules |
variantEffectPredictor.subsetVcf_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |
variantEffectPredictor.chromosomeArray_timeout |
Int |
1 |
Maximum amount of time (in hours) the task can run for. |
variantEffectPredictor.chromosomeArray_threads |
Int |
4 |
Requested CPU threads. |
variantEffectPredictor.chromosomeArray_jobMemory |
Int |
1 |
Memory allocated to job (in GB). |
variantEffectPredictor.getSampleNames_timeout |
Int |
6 |
Hours before task timeout |
variantEffectPredictor.getSampleNames_threads |
Int |
4 |
Requested CPU threads |
variantEffectPredictor.getSampleNames_jobMemory |
Int |
32 |
Memory allocated for this job (GB) |
variantEffectPredictor.getSampleNames_modules |
String |
"vcftools/0.1.16" |
Required environment modules |
variantEffectPredictor.getSampleNames_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |
variantEffectPredictor.targetBedTask_timeout |
Int |
6 |
Hours before task timeout |
variantEffectPredictor.targetBedTask_threads |
Int |
4 |
Requested CPU threads |
variantEffectPredictor.targetBedTask_jobMemory |
Int |
32 |
Memory allocated for this job (GB) |
variantEffectPredictor.targetBedTask_modules |
String |
"bedtools/2.27 tabix/0.2.6" |
Required environment modules |
variantEffectPredictor.targetBedTask_basename |
String |
basename("~{vcfFile}",".vcf.gz") |
Base name |