R/manta.R
In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems
Defines functions
call_somatic_sv_manta
annotate_output_manta
call_germline_sv_manta
call_sv_manta
Documented in
annotate_output_manta
call_germline_sv_manta
call_somatic_sv_manta
call_sv_manta
#' Strelka wrapper for SNV variant calling
#'
#' This function wraps the STRELKA functions for variant calling
#'
#' @param bin_strelka_somatic Path to strelka somatic workflow binary
#' @param bin_strelka_germline Path to strelka germline workflow binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param variants [REQUIRED] Variants types to call. Default all. Options ["snv","sv","all"]
#' @param indel_candidates [OPTIONAL] Path to indel candidates file produced by MANTA.
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
call_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
cache_vep=build_default_cache_list()$cache_vep,
tumour=NULL,
normal=NULL,
regions=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
chromosomes=c(1:22,"X","Y","MT"),
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
normal_id=NULL,
tumour_id=NULL,
patient_id=NULL,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$steps[[fn_id]]<-.this.env
.main.step<-.main$steps[[fn_id]]
if(!is.null(normal)){
if(is.null(normal_id)){
normal_id=get_file_name(normal)
}
if(!is.null(tumour)){
if(is.null(tumour_id)){
tumour_id=get_file_name(tumour)
}
.main.step$steps<-append(
.main.step$steps,
call_somatic_sv_manta(
bin_samtools=bin_samtools,
bin_manta=bin_manta,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
tumour=input,
normal=normal,
annotate=annotate,
tabulate=tabulate,
ref_genome=ref_genome,
chromosomes=chromosomes,
regions=regions,
patient_id=patient_id,
tumour_id=tumour_id,
normal_id=normal_id,
output_dir=paste0(out_file_dir,"/",input_id,"/somatic/sv"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
targeted=targeted,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$call_somatic_sv_manta
.main.step$out_files$somatic=.this.step$out_files
}else{
.main.step$steps<-append(
.main.step$steps,
call_germline_sv_manta(
bin_samtools=bin_samtools,
bin_manta=bin_manta,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
normal=input,
annotate=annotate,
patient_id=patient_id,
chromosomes=chromosomes,
regions=regions,
normal_id=normal_id,
tabulate=tabulate,
ref_genome=ref_genome,
output_dir=paste0(out_file_dir,"/",input_id,"/germline/sv"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
targeted=targeted,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$call_germline_sv_manta
.main.step$out_files$germline=.this.step$out_files
}
}
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars=ifelse(!is.null(tumour),"tumour","normal")
)
launch(.env=.base.env)
}
#' Manta wrapper for structural variant calling
#'
#' This function wraps the Manta workflow functions for structural variant calling
#'
#' @param bin_manta Path to manta pipeline binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
call_germline_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
normal=NULL,
normal_id=NULL,
patient_id=NULL,
regions=NULL,
chromosomes=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$exec_code=paste0(
bin_manta,
" --bam ",normalizePath(input),
" --referenceFasta ", normalizePath(ref_genome) ,
" --runDir ", out_file_dir,
ifelse(!is.null(regions),paste0(" --callRegions ",regions),""),
ifelse(targeted," --exome ",""), "; ",
paste0(
out_file_dir,
"/runWorkflow.py -m local -j ",
threads)
)
.main$out_files$manta$workflow=paste0(out_file_dir,"/runWorkflow.py")
.main$out_files$manta$stats=list(
tsv=paste0(out_file_dir,"/results/stats/runStats.tsv"),
xml=paste0(out_file_dir,"/results/stats/runStats.xml")
)
.main$out_files$manta$variants=list(
indel_candidate=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz"),
indel_candidate_idx=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz.tbi"),
diploid_sv=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz"),
diploid_sv_idx=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz.tbi")
)
run_job(
.env=.this.env
)
.main.step=.main$steps[[fn_id]]
### We don't split by chromosome because its not necessary as SV files are not large enough
.main.step$steps=append(.main.step$steps,
annotate_output_manta(
vcf=.main.step$out_files$manta$variants$diploid_sv,
bin_samtools=bin_samtools,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
annotate=annotate,
output_dir=out_file_dir,
patient_id=patient_id,
normal_id=normal_id,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars="normal"
)
launch(.env=.base.env)
}
#' Strelka wrapper for germline SNV variant calling
#'
#' This function wraps the STRELKA functions for germline variant calling
#'
#' @param bin_strelka_somatic Path to strelka somatic workflow binary
#' @param tumour [OPTIONAL] Path to tumour BAM file.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param variants [REQUIRED] Variants types to call. Default all. Options ["snv","sv","all"]
#' @param indel_candidates [OPTIONAL] Path to indel candidates file produced by MANTA.
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
annotate_output_manta<-function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
chromosomes=NULL,
vcf=NULL,
annotate=TRUE,
patient_id=NULL,
tumour_id=NULL,
normal_id=NULL,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main.step=.main$steps[[fn_id]]
if(!is.null(chromosomes)){
chromosomes=input
}else{
vcf=input
}
.main.step$steps <- append(
.main.step$steps,
add_af_strelka_vcf(
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
vcf=vcf,
output_dir=paste0(out_file_dir,"/annotated/af"),
type="sv",
fn_id="sv",
chromosomes=chromosomes,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$add_af_strelka_vcf.sv
.main.step$out_files$annotated$af=.this.step$out_files
.main.step$steps <-append(
.main.step$steps,
extract_pass_variants_strelka_vcf(
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
vcf=.main.step$out_files$annotated$af$bgzip_vcf,
type="sv",
fn_id="sv",
chromosomes=chromosomes,
output_dir=paste0(out_file_dir,"/annotated/filter"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$extract_pass_variants_strelka_vcf.sv
.main.step$out_files$annotated$filter=.this.step$out_files
if(annotate){
.main.step$steps<-append(
.main.step$steps,
annotate_strelka_vep(
bin_vep=bin_vep,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
cache_vep=cache_vep,
patient_id=patient_id,
normal_id=normal_id,
tumour_id=tumour_id,
vcf=.main.step$out_files$annotated$filter$bgzip_vcf,
type="sv",
fn_id="sv",
chromosomes=chromosomes,
output_dir=paste0(out_file_dir,"/annotated/vep"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$annotate_strelka_vep.sv
.main.step$out_files$annotated$vep=.this.step$out_files
}
.env$.main<-.main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars=ifelse(!is.null(chromosomes),"chromosomes","vcf")
)
launch(.env=.base.env)
}
#' Manta wrapper for structural variant calling
#'
#' This function wraps the Manta workflow functions for structural variant calling
#'
#' @param bin_manta Path to manta pipeline binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @export
call_somatic_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
tumour=NULL,
normal=NULL,
normal_id=NULL,
tumour_id=NULL,
patient_id=NULL,
regions=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$exec_code=paste0(
bin_manta,
" --tumorBam ",input,
" --normalBam ",normal,
" --referenceFasta ", ref_genome ,
" --runDir ", out_file_dir,
ifelse(!is.null(regions),paste0(" --callRegions ",regions),""),
ifelse(targeted," --exome ",""),"; ",
paste0(
out_file_dir,
"/runWorkflow.py -m local -j ",
threads)
)
.main$out_files$manta$workflow=paste0(out_file_dir,"/runWorkflow.py")
.main$out_files$manta$stats=list(
tsv=paste0(out_file_dir,"/results/stats/runStats.tsv"),
xml=paste0(out_file_dir,"/results/stats/runStats.xml")
)
.main$out_files$manta$variants=list(
sv=paste0(out_file_dir,"/results/variants/somaticSV.vcf.gz"),
sv_idx=paste0(out_file_dir,"/results/variants/somaticSV.vcf.gz"),
indel_candidates=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz"),
indel_candidates_idx=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz.tbi"),
sv_candidate=paste0(out_file_dir,"/results/variants/candidateSV.vcf.gz"),
sv_candidate_index=paste0(out_file_dir,"/results/variants/candidateSV.vcf.gz.tbi"),
diploid_sv=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz"),
diploid_sv_idx=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz.tbi")
)
run_job(
.env=.this.env
)
.main.step=.main$steps[[fn_id]]
### We don't split by chromosome because its not necessary as SV files are not large enough
.main.step$steps=append(.main.step$steps,
annotate_output_manta(
vcf=.main.step$out_files$manta$variants$sv,
bin_samtools=bin_samtools,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
patient_id=patient_id,
tumour_id=tumour_id,
normal_id=normal_id,
cache_vep=cache_vep,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars="tumour"
)
launch(.env=.base.env)
}
TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.
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Defines functions call_somatic_sv_manta annotate_output_manta call_germline_sv_manta call_sv_manta
Documented in annotate_output_manta call_germline_sv_manta call_somatic_sv_manta call_sv_manta
#' Strelka wrapper for SNV variant calling
#'
#' This function wraps the STRELKA functions for variant calling
#'
#' @param bin_strelka_somatic Path to strelka somatic workflow binary
#' @param bin_strelka_germline Path to strelka germline workflow binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param variants [REQUIRED] Variants types to call. Default all. Options ["snv","sv","all"]
#' @param indel_candidates [OPTIONAL] Path to indel candidates file produced by MANTA.
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
call_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
cache_vep=build_default_cache_list()$cache_vep,
tumour=NULL,
normal=NULL,
regions=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
chromosomes=c(1:22,"X","Y","MT"),
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
normal_id=NULL,
tumour_id=NULL,
patient_id=NULL,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$steps[[fn_id]]<-.this.env
.main.step<-.main$steps[[fn_id]]
if(!is.null(normal)){
if(is.null(normal_id)){
normal_id=get_file_name(normal)
}
if(!is.null(tumour)){
if(is.null(tumour_id)){
tumour_id=get_file_name(tumour)
}
.main.step$steps<-append(
.main.step$steps,
call_somatic_sv_manta(
bin_samtools=bin_samtools,
bin_manta=bin_manta,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
tumour=input,
normal=normal,
annotate=annotate,
tabulate=tabulate,
ref_genome=ref_genome,
chromosomes=chromosomes,
regions=regions,
patient_id=patient_id,
tumour_id=tumour_id,
normal_id=normal_id,
output_dir=paste0(out_file_dir,"/",input_id,"/somatic/sv"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
targeted=targeted,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$call_somatic_sv_manta
.main.step$out_files$somatic=.this.step$out_files
}else{
.main.step$steps<-append(
.main.step$steps,
call_germline_sv_manta(
bin_samtools=bin_samtools,
bin_manta=bin_manta,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
normal=input,
annotate=annotate,
patient_id=patient_id,
chromosomes=chromosomes,
regions=regions,
normal_id=normal_id,
tabulate=tabulate,
ref_genome=ref_genome,
output_dir=paste0(out_file_dir,"/",input_id,"/germline/sv"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
targeted=targeted,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$call_germline_sv_manta
.main.step$out_files$germline=.this.step$out_files
}
}
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars=ifelse(!is.null(tumour),"tumour","normal")
)
launch(.env=.base.env)
}
#' Manta wrapper for structural variant calling
#'
#' This function wraps the Manta workflow functions for structural variant calling
#'
#' @param bin_manta Path to manta pipeline binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
call_germline_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
normal=NULL,
normal_id=NULL,
patient_id=NULL,
regions=NULL,
chromosomes=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$exec_code=paste0(
bin_manta,
" --bam ",normalizePath(input),
" --referenceFasta ", normalizePath(ref_genome) ,
" --runDir ", out_file_dir,
ifelse(!is.null(regions),paste0(" --callRegions ",regions),""),
ifelse(targeted," --exome ",""), "; ",
paste0(
out_file_dir,
"/runWorkflow.py -m local -j ",
threads)
)
.main$out_files$manta$workflow=paste0(out_file_dir,"/runWorkflow.py")
.main$out_files$manta$stats=list(
tsv=paste0(out_file_dir,"/results/stats/runStats.tsv"),
xml=paste0(out_file_dir,"/results/stats/runStats.xml")
)
.main$out_files$manta$variants=list(
indel_candidate=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz"),
indel_candidate_idx=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz.tbi"),
diploid_sv=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz"),
diploid_sv_idx=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz.tbi")
)
run_job(
.env=.this.env
)
.main.step=.main$steps[[fn_id]]
### We don't split by chromosome because its not necessary as SV files are not large enough
.main.step$steps=append(.main.step$steps,
annotate_output_manta(
vcf=.main.step$out_files$manta$variants$diploid_sv,
bin_samtools=bin_samtools,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
cache_vep=cache_vep,
annotate=annotate,
output_dir=out_file_dir,
patient_id=patient_id,
normal_id=normal_id,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars="normal"
)
launch(.env=.base.env)
}
#' Strelka wrapper for germline SNV variant calling
#'
#' This function wraps the STRELKA functions for germline variant calling
#'
#' @param bin_strelka_somatic Path to strelka somatic workflow binary
#' @param tumour [OPTIONAL] Path to tumour BAM file.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param variants [REQUIRED] Variants types to call. Default all. Options ["snv","sv","all"]
#' @param indel_candidates [OPTIONAL] Path to indel candidates file produced by MANTA.
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @param output_dir [OPTIONAL] Path to the output directory. Default current directory
#' @param threads [OPTIONAL] Number of threads to split the work. Default 4
#' @param batch_config [OPTIONAL] Default configuration for job submission in batch.
#' @param ram [OPTIONAL] RAM memory to asing to each thread. Default 4
#' @param verbose [OPTIONAL] Enables progress messages. Default False.
#' @param mode [REQUIRED] Where to parallelize. Default local. Options ["local","batch"]
#' @param executor_id Task EXECUTOR ID. Default "recalCovariates"
#' @param task_name Task name. Default "recalCovariates"
#' @param time [OPTIONAL] If batch mode. Max run time per job. Default "48:0:0"
#' @param update_time [OPTIONAL] If batch mode. Job update time in seconds. Default 60.
#' @param wait [OPTIONAL] If batch mode wait for batch to finish. Default FALSE
#' @param hold [OPTIONAL] HOld job until job is finished. Job ID.
#' @export
annotate_output_manta<-function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
chromosomes=NULL,
vcf=NULL,
annotate=TRUE,
patient_id=NULL,
tumour_id=NULL,
normal_id=NULL,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main.step=.main$steps[[fn_id]]
if(!is.null(chromosomes)){
chromosomes=input
}else{
vcf=input
}
.main.step$steps <- append(
.main.step$steps,
add_af_strelka_vcf(
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
vcf=vcf,
output_dir=paste0(out_file_dir,"/annotated/af"),
type="sv",
fn_id="sv",
chromosomes=chromosomes,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$add_af_strelka_vcf.sv
.main.step$out_files$annotated$af=.this.step$out_files
.main.step$steps <-append(
.main.step$steps,
extract_pass_variants_strelka_vcf(
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
vcf=.main.step$out_files$annotated$af$bgzip_vcf,
type="sv",
fn_id="sv",
chromosomes=chromosomes,
output_dir=paste0(out_file_dir,"/annotated/filter"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$extract_pass_variants_strelka_vcf.sv
.main.step$out_files$annotated$filter=.this.step$out_files
if(annotate){
.main.step$steps<-append(
.main.step$steps,
annotate_strelka_vep(
bin_vep=bin_vep,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
cache_vep=cache_vep,
patient_id=patient_id,
normal_id=normal_id,
tumour_id=tumour_id,
vcf=.main.step$out_files$annotated$filter$bgzip_vcf,
type="sv",
fn_id="sv",
chromosomes=chromosomes,
output_dir=paste0(out_file_dir,"/annotated/vep"),
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.this.step=.main.step$steps$annotate_strelka_vep.sv
.main.step$out_files$annotated$vep=.this.step$out_files
}
.env$.main<-.main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars=ifelse(!is.null(chromosomes),"chromosomes","vcf")
)
launch(.env=.base.env)
}
#' Manta wrapper for structural variant calling
#'
#' This function wraps the Manta workflow functions for structural variant calling
#'
#' @param bin_manta Path to manta pipeline binary
#' @param tumour [OPTIONAL] Path to tumour BAM file. If not given will assume germline variant calling.
#' @param normal [REQUIRED] Path to tumour BAM file.
#' @param ref_genome [REQUIRED] Path to reference genome FASTA
#' @param targeted [REQUIRED] Remove coverage filtering for exome/targeted data. Default TRUE
#' @export
call_somatic_sv_manta=function(
bin_samtools=build_default_tool_binary_list()$bin_samtools,
bin_bcftools=build_default_tool_binary_list()$bin_bcftools,
bin_bgzip=build_default_tool_binary_list()$bin_bgzip,
bin_tabix=build_default_tool_binary_list()$bin_tabix,
bin_vep=build_default_tool_binary_list()$bin_vep,
cache_vep=build_default_cache_list()$cache_vep,
bin_manta=build_default_tool_binary_list()$bin_manta,
tumour=NULL,
normal=NULL,
normal_id=NULL,
tumour_id=NULL,
patient_id=NULL,
regions=NULL,
ref_genome=build_default_reference_list()$HG19$reference$genome,
targeted=TRUE,
annotate=TRUE,
tabulate=TRUE,
...
){
run_main=function(
.env
){
.this.env=environment()
append_env(to=.this.env,from=.env)
set_main(.env=.this.env)
.main$exec_code=paste0(
bin_manta,
" --tumorBam ",input,
" --normalBam ",normal,
" --referenceFasta ", ref_genome ,
" --runDir ", out_file_dir,
ifelse(!is.null(regions),paste0(" --callRegions ",regions),""),
ifelse(targeted," --exome ",""),"; ",
paste0(
out_file_dir,
"/runWorkflow.py -m local -j ",
threads)
)
.main$out_files$manta$workflow=paste0(out_file_dir,"/runWorkflow.py")
.main$out_files$manta$stats=list(
tsv=paste0(out_file_dir,"/results/stats/runStats.tsv"),
xml=paste0(out_file_dir,"/results/stats/runStats.xml")
)
.main$out_files$manta$variants=list(
sv=paste0(out_file_dir,"/results/variants/somaticSV.vcf.gz"),
sv_idx=paste0(out_file_dir,"/results/variants/somaticSV.vcf.gz"),
indel_candidates=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz"),
indel_candidates_idx=paste0(out_file_dir,"/results/variants/candidateSmallIndels.vcf.gz.tbi"),
sv_candidate=paste0(out_file_dir,"/results/variants/candidateSV.vcf.gz"),
sv_candidate_index=paste0(out_file_dir,"/results/variants/candidateSV.vcf.gz.tbi"),
diploid_sv=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz"),
diploid_sv_idx=paste0(out_file_dir,"/results/variants/diploidSV.vcf.gz.tbi")
)
run_job(
.env=.this.env
)
.main.step=.main$steps[[fn_id]]
### We don't split by chromosome because its not necessary as SV files are not large enough
.main.step$steps=append(.main.step$steps,
annotate_output_manta(
vcf=.main.step$out_files$manta$variants$sv,
bin_samtools=bin_samtools,
bin_bcftools=bin_bcftools,
bin_bgzip=bin_bgzip,
bin_tabix=bin_tabix,
bin_vep=bin_vep,
patient_id=patient_id,
tumour_id=tumour_id,
normal_id=normal_id,
cache_vep=cache_vep,
tmp_dir=tmp_dir,
env_dir=env_dir,
batch_dir=batch_dir,
err_msg=err_msg,
verbose=verbose,
threads=threads,
ram=ram,
executor_id=task_id
)
)
.env$.main <- .main
}
.base.env=environment()
list2env(list(...),envir=.base.env)
set_env_vars(
.env= .base.env,
vars="tumour"
)
launch(.env=.base.env)
}
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