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pughlab_dnaseq_germline_pipeline.pl
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pughlab_dnaseq_germline_pipeline.pl
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#!/usr/bin/env perl
### pughlab_dnaseq_germline_pipeline.pl ############################################################
use AutoLoader 'AUTOLOAD';
use strict;
use warnings;
use Carp;
use POSIX qw(strftime);
use Getopt::Std;
use Getopt::Long;
use File::Basename;
use File::Path qw(make_path);
use YAML qw(LoadFile);
use List::Util qw(any none);
use Data::Dumper;
my $cwd = dirname(__FILE__);
require "$cwd/scripts/utilities.pl";
####################################################################################################
# version author comment
# 1.0 sprokopec script to run PughLab DNASeq Germline pipeline
### USAGE ##########################################################################################
# pughlab_dnaseq_germline_pipeline.pl -c tool_config.yaml -d data.yaml
#
# where:
# - tool_config.yaml contains tool versions and parameters, output directory, reference
# information, etc.
# - data_config.yaml contains sample information (YAML file containing paths to FASTQ files,
# generated by create_fastq_yaml.pl)
### SUBROUTINES ####################################################################################
### MAIN ###########################################################################################
sub main {
my %args = (
tool_config => undef,
data_config => undef,
step1 => undef,
step2 => undef,
step3 => undef,
step4 => undef,
step5 => undef,
cleanup => undef,
cluster => undef,
dry_run => undef,
@_
);
my $tool_config = $args{tool_config};
my $data_config = $args{data_config};
### PREAMBLE ######################################################################################
# load tool config
my $tool_data = LoadFile($tool_config);
my $date = strftime "%F", localtime;
my $timestamp = strftime "%F_%H-%M-%S", localtime;
# check for and/or create output directories
my $output_directory = $tool_data->{output_dir};
$output_directory =~ s/\/$//;
my $log_directory = join('/', $output_directory, 'logs', 'run_DNA_pipeline_' . $timestamp);
unless(-e $output_directory) { make_path($output_directory); }
unless(-e $log_directory) { make_path($log_directory); }
# start logging
my $log_file = join('/', $log_directory, 'run_DNASeq_pipeline.log');
open (my $log, '>', $log_file) or die "Could not open $log_file for writing.";
print $log "---\n";
print $log "Running PughLab DNA-Seq pipeline.\n";
print $log "\n Tool config used: $tool_config";
print $log "\n Sample config used: $data_config";
print $log "\n Output directory: $output_directory";
print $log "\n---\n\n";
my $seq_type = $tool_data->{seq_type};
# indicate maximum time limit for parent jobs to wait
my $max_time = '5-00:00:00';
if ('wgs' eq $tool_data->{seq_type}) { $max_time = '21-00:00:00'; }
if ('targeted' eq $tool_data->{seq_type}) { $max_time = '3-00:00:00'; }
my $perl = 'perl/' . $tool_data->{perl_version};
my $samtools = 'samtools/' . $tool_data->{samtools_version};
# get optional HPC group
my $hpc_group = defined($tool_data->{hpc_group}) ? "-A $tool_data->{hpc_group}" : undef;
### MAIN ###########################################################################################
my $run_script;
my ($fastqc_run_id, $bwa_run_id, $gatk_run_id, $qc_run_id, $coverage_run_id, $hc_run_id);
my ($strelka_run_id, $mutect_run_id, $mutect2_run_id, $varscan_run_id, $vardict_run_id);
my ($delly_run_id, $manta_run_id, $gatk_cnv_run_id, $svict_run_id);
my ($hc_run_id1, $erds_run_id, $mavis_run_id, $report_run_id);
my (@step1_job_ids, @step2_job_ids, @step3_job_ids, @step4_job_ids, @job_ids);
my $current_dependencies = '';
# prepare directory structure
my $fastqc_directory = join('/', $output_directory, 'fastqc');
my $bwa_directory = join('/', $output_directory, 'BWA');
my $gatk_directory = join('/', $output_directory, 'GATK');
my $gatk_cnv_directory = join('/', $output_directory, 'GATK_CNV');
my $qc_directory = join('/', $output_directory, 'BAMQC', 'SequenceMetrics');
my $coverage_directory = join('/', $output_directory, 'BAMQC', 'Coverage');
my $hc_directory = join('/', $output_directory, 'HaplotypeCaller');
my $strelka_directory = join('/', $output_directory, 'Strelka');
my $erds_directory = join('/', $output_directory, 'ERDS');
my $manta_directory = join('/', $output_directory, 'Manta');
my $mutect_directory = join('/', $output_directory, 'MuTect');
my $mutect2_directory = join('/', $output_directory, 'MuTect2');
my $varscan_directory = join('/', $output_directory, 'VarScan');
my $vardict_directory = join('/', $output_directory, 'VarDict');
my $delly_directory = join('/', $output_directory, 'Delly');
my $svict_directory = join('/', $output_directory, 'SViCT');
my $mavis_directory = join('/', $output_directory, 'Mavis');
# check which tools have been requested
my %tool_set = (
'fastqc' => defined($tool_data->{fastqc}->{run}) ? $tool_data->{fastqc}->{run} : 'N',
'bwa' => defined($tool_data->{bwa}->{run}) ? $tool_data->{bwa}->{run} : 'N',
'gatk' => defined($tool_data->{gatk}->{run}) ? $tool_data->{gatk}->{run} : 'N',
'bamqc' => defined($tool_data->{bamqc}->{run}) ? $tool_data->{bamqc}->{run} : 'N',
'haplotype_caller' => defined($tool_data->{haplotype_caller}->{run}) ? $tool_data->{haplotype_caller}->{run} : 'N',
'mutect' => defined($tool_data->{mutect}->{run}) ? $tool_data->{mutect}->{run} : 'N',
'mutect2' => defined($tool_data->{mutect2}->{run}) ? $tool_data->{mutect2}->{run} : 'N',
'strelka' => defined($tool_data->{strelka}->{run}) ? $tool_data->{strelka}->{run} : 'N',
'varscan' => defined($tool_data->{varscan}->{run}) ? $tool_data->{varscan}->{run} : 'N',
'vardict' => defined($tool_data->{vardict}->{run}) ? $tool_data->{vardict}->{run} : 'N',
'gatk_cnv' => defined($tool_data->{gatk_cnv}->{run}) ? $tool_data->{gatk_cnv}->{run} : 'N',
'delly' => defined($tool_data->{delly}->{run}) ? $tool_data->{delly}->{run} : 'N',
'manta' => defined($tool_data->{manta}->{run}) ? $tool_data->{manta}->{run} : 'N',
'svict' => defined($tool_data->{svict}->{run}) ? $tool_data->{svict}->{run} : 'N',
'erds' => defined($tool_data->{erds}->{run}) ? $tool_data->{erds}->{run} : 'N',
'mavis' => defined($tool_data->{mavis}->{run}) ? $tool_data->{mavis}->{run} : 'N'
);
print $log Dumper \%tool_set;
# indicate YAML files for processed BAMs
my $bwa_output_yaml = join('/', $bwa_directory, 'bwa_bam_config_' . $timestamp . '.yaml');
my $gatk_output_yaml = join('/', $gatk_directory, 'gatk_bam_config_' . $timestamp . '.yaml');
# are we running step1 (alignments) or are BAMs provided as input?
if ( (!$args{step1}) ) {
$gatk_output_yaml = $data_config;
}
if ( (!$args{step4}) && ($args{step5}) ) {
print $log "Can not make final report without summarizing output; setting --summarize to true";
$args{step4} = 1;
}
# Should pre-processing (fastqc, alignment + GATK indel realignment/recalibration) be performed?
if ($args{step1}) {
## run FASTQC pipeline
unless(-e $fastqc_directory) { make_path($fastqc_directory); }
if ('Y' eq $tool_set{'fastqc'}) {
my $fastqc_command = join(' ',
"perl $cwd/scripts/collect_fastqc_metrics.pl",
"-o", $fastqc_directory,
"-t", $tool_config,
"-d", $data_config,
"-c", $args{cluster}
);
# record command (in log directory) and then run job
print $log "Submitting job for collect_fastqc_metrics.pl\n";
print $log " COMMAND: $fastqc_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_fastqc',
cmd => $fastqc_command,
modules => [$perl],
mem => '256M',
max_time => '48:00:00',
hpc_driver => $args{cluster},
extra_args => [$hpc_group]
);
if ($args{dry_run}) {
$fastqc_command .= " --dry-run";
`$fastqc_command`;
$fastqc_run_id = 'pughlab_dna_pipeline__run_fastqc';
} else {
$fastqc_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> FASTQC job id: $fastqc_run_id\n\n";
push @job_ids, $fastqc_run_id;
}
}
## run BWA-alignment pipeline
unless(-e $bwa_directory) { make_path($bwa_directory); }
if ('Y' eq $tool_set{'bwa'}) {
my $bwa_command = join(' ',
"perl $cwd/scripts/bwa.pl",
"-o", $bwa_directory,
"-t", $tool_config,
"-d", $data_config,
"-b", $bwa_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$bwa_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for bwa.pl\n";
print $log " COMMAND: $bwa_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_bwa',
cmd => $bwa_command,
modules => [$perl],
mem => '256M',
max_time => $max_time,
hpc_driver => $args{cluster},
extra_args => [$hpc_group]
);
if ($args{dry_run}) {
$bwa_command .= " --dry-run";
`$bwa_command`;
$bwa_run_id = 'pughlab_dna_pipeline__run_bwa';
} else {
$bwa_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> BWA job id: $bwa_run_id\n\n";
push @step1_job_ids, $bwa_run_id;
push @job_ids, $bwa_run_id;
}
}
## run GATK indel realignment/recalibration pipeline
unless(-e $gatk_directory) { make_path($gatk_directory); }
if ('Y' eq $tool_set{'gatk'}) {
my $gatk_command = join(' ',
"perl $cwd/scripts/gatk.pl",
"-o", $gatk_directory,
"-t", $tool_config,
"-d", $bwa_output_yaml,
"-c", $args{cluster},
"-b", $gatk_output_yaml
);
if ($args{cleanup}) {
$gatk_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for gatk.pl\n";
print $log " COMMAND: $gatk_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_gatk',
cmd => $gatk_command,
modules => [$perl],
dependencies => $bwa_run_id,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$gatk_command .= " --dry-run";
`$gatk_command`;
$gatk_run_id = 'pughlab_dna_pipeline__run_gatk';
} else {
$gatk_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> GATK job id: $gatk_run_id\n\n";
push @step1_job_ids, $gatk_run_id;
push @job_ids, $gatk_run_id;
}
}
}
# make sure the dependency isn't empty
if (scalar(@step1_job_ids) > 0) {
$current_dependencies = join(':', @step1_job_ids);
} else {
$current_dependencies = '';
}
## run GATK's CalculateContamination and DepthOfCoverage
## also collect alignment metrics, and calculate callable Bases
if ($args{step2}) {
unless(-e $qc_directory) { make_path($qc_directory); }
unless(-e $coverage_directory) { make_path($coverage_directory); }
if ('Y' eq $tool_set{'bamqc'}) {
# QC (GATK v4.x) pipeline
my $qc_command = join(' ',
"perl $cwd/scripts/get_sequencing_metrics.pl",
"-o", $qc_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$qc_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for get_sequencing_metrics.pl\n";
print $log " COMMAND: $qc_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_qc',
cmd => $qc_command,
modules => [$perl],
dependencies => join(':', @step1_job_ids),
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$qc_command .= " --dry-run";
`$qc_command`;
$qc_run_id = 'pughlab_dna_pipeline__run_qc';
} else {
$qc_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> QC job id: $qc_run_id\n\n";
push @step2_job_ids, $qc_run_id;
push @job_ids, $qc_run_id;
}
# Coverage (GATK, any version) + callable bases pipeline
my $coverage_command = join(' ',
"perl $cwd/scripts/get_coverage.pl",
"-o", $coverage_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$coverage_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for get_coverage.pl\n";
print $log " COMMAND: $coverage_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_coverage',
cmd => $coverage_command,
modules => [$perl],
dependencies => join(':', @step1_job_ids),
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$coverage_command .= " --dry-run";
`$coverage_command`;
$coverage_run_id = 'pughlab_dna_pipeline__run_coverage';
} else {
$coverage_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> Coverage job id: $coverage_run_id\n\n";
push @step2_job_ids, $coverage_run_id;
push @job_ids, $coverage_run_id;
}
}
}
# make sure the dependency isn't empty
if (scalar(@step2_job_ids) > 0) {
$current_dependencies = join(':', @step2_job_ids);
} # else will leave as step1 jobs (or blank)
########################################################################################
# From here on out, it makes more sense to run everything as a single batch.
########################################################################################
if ($args{step3}) {
## run GATK's HaplotypeCaller pipeline
if ('Y' eq $tool_set{'haplotype_caller'}) {
unless(-e $hc_directory) { make_path($hc_directory); }
$hc_run_id = '';
my $hc_command = join(' ',
"perl $cwd/scripts/haplotype_caller.pl",
"-o", $hc_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$hc_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for haplotype_caller.pl\n";
print $log " COMMAND: $hc_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_haplotypecaller',
cmd => $hc_command,
modules => [$perl],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$hc_command .= " --dry-run";
`$hc_command`;
$hc_run_id = 'pughlab_dna_pipeline__run_haplotypecaller';
} else {
$hc_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> HaplotypeCaller job id: $hc_run_id\n\n";
push @step3_job_ids, $hc_run_id;
push @job_ids, $hc_run_id;
}
$hc_run_id1 = $hc_run_id;
# next step will run Genotype GVCFs, and filter final output
$hc_command = join(' ',
"perl $cwd/scripts/genotype_gvcfs.pl",
"-o", $hc_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$hc_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for genotype_gvcfs.pl\n";
print $log " COMMAND: $hc_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_genotype_gvcfs',
cmd => $hc_command,
modules => [$perl],
dependencies => join(':', $current_dependencies, $hc_run_id),
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$hc_command .= " --dry-run";
`$hc_command`;
$hc_run_id = 'pughlab_dna_pipeline__run_genotype_gvcfs';
} else {
$hc_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> GenotypeGVCFs job id: $hc_run_id\n\n";
push @job_ids, $hc_run_id;
}
# finally, annotate and filter using CPSR/PCGR
$hc_command = join(' ',
"perl $cwd/scripts/annotate_germline.pl",
"-o", $hc_directory,
"-i", join('/', $hc_directory, 'cohort'),
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$hc_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for annotate_germline.pl\n";
print $log " COMMAND: $hc_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_annotate_germline',
cmd => $hc_command,
modules => [$perl],
dependencies => join(':', $current_dependencies, $hc_run_id),
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$hc_run_id = 'pughlab_dna_pipeline__run_annotate_germline';
} else {
$hc_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> AnnotateGermline job id: $hc_run_id\n\n";
push @job_ids, $hc_run_id;
}
}
## run STRELKA pipeline
if ('Y' eq $tool_set{'strelka'}) {
unless(-e $strelka_directory) { make_path($strelka_directory); }
# run the panel of normals function to get germline calls
my $strelka_command = join(' ',
"perl $cwd/scripts/strelka.pl",
"-o", $strelka_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"--create-panel-of-normals",
"-c", $args{cluster}
);
if ($args{cleanup}) {
$strelka_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for strelka.pl --create-panel-of-normals\n";
print $log " COMMAND: $strelka_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_strelka_pon',
cmd => $strelka_command,
modules => [$perl, $samtools],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$strelka_command .= " --dry-run";
`$strelka_command`;
$strelka_run_id = 'pughlab_dna_pipeline__run_strelka_pon';
} else {
$strelka_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> Strelka PoN job id: $strelka_run_id\n\n";
push @step3_job_ids, $strelka_run_id;
push @job_ids, $strelka_run_id;
}
}
## run GATK's MuTect pipeline
if ('Y' eq $tool_set{'mutect'}) {
unless(-e $mutect_directory) { make_path($mutect_directory); }
# run the panel of normals function to get germline calls
my $mutect_command = join(' ',
"perl $cwd/scripts/mutect.pl",
"-o", $mutect_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster},
"--create-panel-of-normals"
);
if ($args{cleanup}) {
$mutect_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for mutect.pl --create-panel-of-normals\n";
print $log " COMMAND: $mutect_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_mutect_pon',
cmd => $mutect_command,
modules => [$perl],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$mutect_command .= " --dry-run";
`$mutect_command`;
$mutect_run_id = 'pughlab_dna_pipeline__run_mutect_pon';
} else {
$mutect_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> MuTect PoN job id: $mutect_run_id\n\n";
push @step3_job_ids, $mutect_run_id;
push @job_ids, $mutect_run_id;
}
}
## also run GATK's newer MuTect2 pipeline
if ('Y' eq $tool_set{'mutect2'}) {
unless(-e $mutect2_directory) { make_path($mutect2_directory); }
# run the panel of normals function to get germline calls
my $mutect2_command = join(' ',
"perl $cwd/scripts/mutect2.pl",
"-o", $mutect2_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster},
"--create-panel-of-normals"
);
if ($args{cleanup}) {
$mutect2_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for mutect2.pl --create-panel-of-normals\n";
print $log " COMMAND: $mutect2_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_mutect2_pon',
cmd => $mutect2_command,
modules => [$perl],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$mutect2_command .= " --dry-run";
`$mutect2_command`;
$mutect2_run_id = 'pughlab_dna_pipeline__run_mutect2_pon';
} else {
$mutect2_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> MuTect2 PoN job id: $mutect2_run_id\n\n";
push @step3_job_ids, $mutect2_run_id;
push @job_ids, $mutect2_run_id;
}
}
## run VarScan SNV/CNV pipeline
if ('Y' eq $tool_set{'varscan'}) {
unless(-e $varscan_directory) { make_path($varscan_directory); }
my $varscan_command = join(' ',
"perl $cwd/scripts/varscan.pl",
"-o", $varscan_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$varscan_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for varscan.pl\n";
print $log " COMMAND: $varscan_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_varscan',
cmd => $varscan_command,
modules => [$perl],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$varscan_command .= " --dry-run";
`$varscan_command`;
$varscan_run_id = 'pughlab_dna_pipeline__run_varscan';
} else {
$varscan_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> VarScan job id: $varscan_run_id\n\n";
push @step3_job_ids, $varscan_run_id;
push @job_ids, $varscan_run_id;
}
}
## run MANTA pipeline
if ('Y' eq $tool_set{'manta'}) {
unless(-e $manta_directory) { make_path($manta_directory); }
# run the panel of normals function to get germline calls
my $manta_command = join(' ',
"perl $cwd/scripts/manta.pl",
"-o", $manta_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster},
"--germline"
);
if ($args{cleanup}) {
$manta_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for manta.pl\n";
print $log " COMMAND: $manta_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_manta',
cmd => $manta_command,
modules => [$perl, $samtools],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$manta_command .= " --dry-run";
`$manta_command`;
$manta_run_id = 'pughlab_dna_pipeline__run_manta';
} else {
$manta_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> Manta job id: $manta_run_id\n\n";
push @step3_job_ids, $manta_run_id;
push @job_ids, $manta_run_id;
}
}
## GATK gCNV pipeline
if ('Y' eq $tool_set{'gatk_cnv'}) {
unless(-e $gatk_cnv_directory) { make_path($gatk_cnv_directory); }
my $gatk_cnv_command = join(' ',
"perl $cwd/scripts/gatk_gcnv.pl",
"-o", $gatk_cnv_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}
);
# record command (in log directory) and then run job
print $log "Submitting job for gatk_gcnv.pl\n";
print $log " COMMAND: $gatk_cnv_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_gatk_gcnv',
cmd => $gatk_cnv_command,
modules => [$perl],
dependencies => $current_dependencies,
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$gatk_cnv_command .= " --dry-run";
`$gatk_cnv_command`;
$gatk_cnv_run_id = 'pughlab_dna_pipeline__run_gatk_gcnv';
} else {
$gatk_cnv_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> GATK gCNV job id: $gatk_cnv_run_id\n\n";
push @step3_job_ids, $gatk_cnv_run_id;
push @job_ids, $gatk_cnv_run_id;
}
}
## ERDS gCNV pipeline
if ('Y' eq $tool_set{'erds'}) {
unless(-e $erds_directory) { make_path($erds_directory); }
my $erds_command = join(' ',
"perl $cwd/scripts/erds_gcnv.pl",
"-o", $erds_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-v", $hc_directory,
"-c", $args{cluster}
);
if ($args{cleanup}) {
$erds_command .= " --remove";
}
# record command (in log directory) and then run job
print $log "Submitting job for erds_gcnv.pl\n";
print $log " COMMAND: $erds_command\n\n";
$run_script = write_script(
log_dir => $log_directory,
name => 'pughlab_dna_pipeline__run_erds',
cmd => $erds_command,
modules => [$perl],
dependencies => join(':', $hc_run_id1, $current_dependencies),
mem => '256M',
max_time => $max_time,
extra_args => [$hpc_group],
hpc_driver => $args{cluster}
);
if ($args{dry_run}) {
$erds_run_id = 'pughlab_dna_pipeline__run_erds';
} else {
$erds_run_id = submit_job(
jobname => $log_directory,
shell_command => $run_script,
hpc_driver => $args{cluster},
dry_run => $args{dry_run},
log_file => $log
);
print $log ">>> ERDS gCNV job id: $erds_run_id\n\n";
push @step3_job_ids, $erds_run_id;
push @job_ids, $erds_run_id;
}
}
## SViCT pipeline
if ('Y' eq $tool_set{'svict'}) {
unless(-e $svict_directory) { make_path($svict_directory); }
my $svict_command = join(' ',
"perl $cwd/scripts/svict.pl",
"-o", $svict_directory,
"-t", $tool_config,
"-d", $gatk_output_yaml,
"-c", $args{cluster}