Skip to content

Commit

Permalink
Merge pull request #256 from uclahs-cds/sfitz-add-F8
Browse files Browse the repository at this point in the history 
Sfitz add F8 and adjust F16 and F32 configs
  • Loading branch information
@sorelfitzgibbon
sorelfitzgibbon authored Jan 12, 2024
2 parents 90e8960 + abd5332 commit 73d6530
Show file tree
Hide file tree
Showing 7 changed files with 178 additions and 38 deletions.
56 changes: 37 additions & 19 deletions config/F16.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,49 +8,67 @@ process {
}
withName: call_sSNV_SomaticSniper {
cpus = 1
memory = 10.GB
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 3.GB
}
}
}
withName: convert_BAM2Pileup_SAMtools {
cpus = 1
memory = 10.GB
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 3.GB
}
}
}
withName: create_IndelCandidate_SAMtools {
cpus = 1
memory = 10.GB
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 3.GB
}
}
}
withName: call_sIndel_Manta {
cpus = 16
memory = 15.GB
cpus = 6
memory = 6.GB
retry_strategy {
memory {
strategy = 'add'
operand = 5.GB
operand = 3.GB
}
}
}
withName: call_sSNV_Strelka2 {
cpus = 16
memory = 15.GB
cpus = 6
memory = 2.GB
retry_strategy {
memory {
strategy = 'add'
operand = 5.GB
operand = 4.GB
}
}
}
withName: call_sSNV_Mutect2 {
cpus = 2
memory = 5.GB
cpus = 1
memory = 3.GB
retry_strategy {
memory {
strategy = 'add'
operand = 5.GB
operand = 2.GB
}
}
}
withName: run_LearnReadOrientationModel_GATK {
cpus = 1
memory = 16.GB
memory = 8.GB
retry_strategy {
memory {
strategy = 'exponential'
Expand All @@ -59,22 +77,22 @@ process {
}
}
withName: call_sSNV_MuSE {
cpus = 10
memory = 16.GB
cpus = 6
memory = 24.GB
retry_strategy {
memory {
strategy = 'add'
operand = 16.GB
operand = 8.GB
}
}
}
withName: run_sump_MuSE {
cpus = 4
memory = 16.GB
cpus = 8
memory = 24.GB
retry_strategy {
memory {
strategy = 'add'
operand = 16.GB
operand = 8.GB
}
}
}
Expand Down
10 changes: 4 additions & 6 deletions config/F2.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,19 +6,19 @@
process {
withName: run_validate_PipeVal {
cpus = 1
memory = 1.GB
memory = 1500.MB
}
withName: call_sSNV_SomaticSniper {
cpus = 1
memory = 3.GB
memory = 1500.MB
}
withName: convert_BAM2Pileup_SAMtools {
cpus = 1
memory = 3.GB
memory = 1500.MB
}
withName: create_IndelCandidate_SAMtools {
cpus = 1
memory = 3.GB
memory = 1500.MB
}
withName: call_sIndel_Manta {
cpus = 2
Expand All @@ -28,10 +28,8 @@ process {
}
withName: plot_VennDiagram_R {
cpus = 2
memory = 1.GB
}
withName: concat_VCFs_BCFtools {
cpus = 2
memory = 2.GB
}
}
6 changes: 3 additions & 3 deletions config/F32.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ process {
retry_strategy {
memory {
strategy = 'add'
operand = 5.GB
operand = 3.GB
}
}
}
Expand All @@ -82,7 +82,7 @@ process {
retry_strategy {
memory {
strategy = 'add'
operand = 10.GB
operand = 16.GB
}
}
}
Expand All @@ -92,7 +92,7 @@ process {
retry_strategy {
memory {
strategy = 'add'
operand = 10.GB
operand = 16.GB
}
}
}
Expand Down
119 changes: 119 additions & 0 deletions config/F8.config
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,119 @@
// Other processes will only run one at a time, so
// we don't need to control their resources.

process {
withName: run_validate_PipeVal {
cpus = 1
memory = 1.GB
}
withName: call_sSNV_SomaticSniper {
cpus = 1
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 2.GB
}
}
}
withName: convert_BAM2Pileup_SAMtools {
cpus = 1
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 2.GB
}
}
}
withName: create_IndelCandidate_SAMtools {
cpus = 1
memory = 1.GB
retry_strategy {
memory {
strategy = 'add'
operand = 2.GB
}
}
}
withName: call_sIndel_Manta {
cpus = 4
memory = 3.GB
retry_strategy {
memory {
strategy = 'add'
operand = 3.GB
}
}
}
withName: call_sSNV_Strelka2 {
cpus = 4
memory = 2.GB
retry_strategy {
memory {
strategy = 'add'
operand = 2.GB
}
}
}
withName: call_sSNV_Mutect2 {
cpus = 1
memory = 3.GB
retry_strategy {
memory {
strategy = 'add'
operand = 2.GB
}
}
}
withName: run_LearnReadOrientationModel_GATK {
cpus = 1
memory = 8.GB
retry_strategy {
memory {
strategy = 'exponential'
operand = 2
}
}
}
withName: call_sSNV_MuSE {
cpus = 4
memory = 10.GB
retry_strategy {
memory {
strategy = 'add'
operand = 6.GB
}
}
}
withName: run_sump_MuSE {
cpus = 4
memory = 12.GB
retry_strategy {
memory {
strategy = 'add'
operand = 4.GB
}
}
}
withName: plot_VennDiagram_R {
cpus = 2
memory = 5.GB
retry_strategy {
memory {
strategy = 'add'
operand = 10.GB
}
}
}
withName: concat_VCFs_BCFtools {
cpus = 2
memory = 5.GB
retry_strategy {
memory {
strategy = 'add'
operand = 10.GB
}
}
}
}
2 changes: 0 additions & 2 deletions config/default.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ params {

//algorithm version
pipeval_version = "4.0.0-rc.2"
samtools_version = "1.16.1"
GATK_version = "4.4.0.0"
somaticsniper_version = "1.0.5.0"
bam_readcount_version = "0.8.0"
Expand All @@ -29,7 +28,6 @@ params {
BCFtools_version = "1.17"
call_ssnv_r_version = "dev"
vcf2maf_version = "v1.6.18"
docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"
docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
docker_image_somaticsniper = "${-> params.docker_container_registry}/somaticsniper:${params.somaticsniper_version}"
Expand Down
21 changes: 14 additions & 7 deletions main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,14 +48,21 @@ log.info """\
normal_out: ${params.samples_to_process.findAll{ it.sample_type == 'normal' }['id']}
"""

if (params.max_cpus < 16 || params.max_memory < 30) {
if (params.max_cpus < 8 || params.max_memory < 16) {
if (params.algorithm.contains('muse') || params.algorithm.contains('mutect2')) {
error """\
------------------------------------
ERROR: Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory.
------------------------------------
To run Mutect2 or MuSE. this pipeline requires at least 16 CPUs and 32 GB of memory.
"""
throw new Exception(
"Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory." +
" To run Mutect2 this pipeline requires at least 8 CPUs and 16 GB of memory." +
" To run MuSE this pipeline requires at least 16 CPUs and 32 GB of memory."
)
}
}
else if (params.max_cpus < 16 || params.max_memory < 32) {
if (params.algorithm.contains('muse')) {
throw new Exception(
"Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory." +
" To run MuSE this pipeline requires at least 16 CPUs and 32 GB of memory."
)
}
}

Expand Down
2 changes: 1 addition & 1 deletion metadata.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ Maintainers: [[email protected]]
Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon']
Languages: ['Docker', 'Nextflow']
Dependencies: ['Docker', 'Nextflow']
Tools: ['GATK 4.4.0.0', 'SomaticSniper v1.0.5.0', 'SAMtools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0.4', 'BCFtools v1.17', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18']
Tools: ['GATK 4.4.0.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0.4', 'BCFtools v1.17', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18']

0 comments on commit 73d6530

Please sign in to comment.