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gnos_upload_vcf.pl
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#!/usr/bin/env perl
use warnings;
use strict;
use feature qw(say);
use autodie;
use IPC::System::Simple qw(system);
use Carp::Always;
use Carp qw( croak );
use Getopt::Long;
use XML::DOM;
use XML::XPath;
use XML::XPath::XMLParser;
use JSON;
use Data::UUID;
use XML::LibXML;
use Time::Piece;
use GNOS::Upload;
use Data::Dumper;
my $milliseconds_in_an_hour = 3600000;
#############################################################################################
# DESCRIPTION #
#############################################################################################
# This tool takes metadata URLs and VCF path(s). It then downloads metadata, #
# parses it, generates submission files, and then performs the uploads. #
# See https://github.com/SeqWare/public-workflows/blob/develop/vcf-uploader/README.md #
# Also see https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+VCF+Submission+SOP+-+v1.0 #
#############################################################################################
# LEFT OFF WITH: working on pipeline JSON
#############
# VARIABLES #
#############
# seconds to wait for a retry
my $cooldown = 60;
# 30 retries at 60 seconds each is 30 hours
my $retries = 30;
# retries for md5sum, 4 hours
my $md5_sleep = 240;
my $vcfs;
my $vcf_types;
my $md5_file = "";
my $vcfs_idx;
my $md5_idx_file = "";
my $tarballs;
my $md5_tarball_file;
# TODO: Sheldon, we will need parameters to the program for the various hard-coded bits below
my $parser = new XML::DOM::Parser;
my $output_dir = "test_output_dir";
my $key = "gnostest.pem";
my $upload_url = "";
my $test = 0;
my $skip_validate = 0;
my $skip_upload = 0;
# hardcoded
my $seqware_version = "1.1.0-alpha.4";
my $workflow_version = "1.0.0";
my $workflow_name = "Workflow_Bundle_Test_Cancer_Variant_Analysis";
# hardcoded
my $workflow_src_url =
"https://github.com/testproject/workflow-test-cancer/tree/$workflow_version/workflow-broad-cancer";
my $workflow_url =
"https://s3.amazonaws.com/oicr.workflow.bundles/released-bundles/Workflow_Bundle_Test_Cancer_Variant_Analysis_"
. $workflow_version
. "_SeqWare_$seqware_version.zip";
my $changelog_url =
"https://github.com/testproject/workflow-test-cancer/blob/$workflow_version/workflow-test-cancer/CHANGELOG.md";
my $force_copy = 0;
my $study_ref_name = "icgc_pancancer_vcf";
my $analysis_center = "OICR";
my $metadata_url;
my $make_runxml = 0;
my $make_expxml = 0;
my $description_file = "";
my $pipeline_json_file = "";
my $qc_json_file = "";
my $timing_json_file = "";
# TODO: check the argument counts here
if ( scalar(@ARGV) < 12 || scalar(@ARGV) > 46 ) {
die "USAGE: 'perl gnos_upload_vcf.pl
--metadata-urls <URLs_for_specimen-level_aligned_BAM_input_comma_sep>
--vcfs <sample-level_vcf_file_path_comma_sep_if_multiple>
--vcf-md5sum-files <file_with_vcf_md5sum_comma_sep_same_order_as_vcfs>
--vcf-idxs <sample-level_vcf_idx_file_path_comma_sep_if_multiple>
--vcf-idx-md5sum-files <file_with_vcf_idx_md5sum_comma_sep_same_order_as_vcfs>
--tarballs <tar.gz_non-vcf_files_comma_sep_if_multiple>
--tarball-md5sum-files <file_with_tarball_md5sum_comma_sep_same_order_as_tarball>
--outdir <output_dir>
--key <gnos.pem>
--upload-url <gnos_server_url>
[--workflow-src-url <http://... the source repo>]
[--workflow-url <http://... the packaged SeqWare Zip>]
[--workflow-name <workflow_name>]
[--workflow-version <workflow_version>]
[--seqware-version <seqware_version_workflow_compiled_with>]
[--description-file <file_path_for_description_txt>]
[--study-refname-override <study_refname_override>]
[--analysis-center-override <analysis_center_override>]
[--pipeline-json <pipeline_json_file>]
[--qc-metrics-json <qc_metrics_json_file>]
[--timing-metrics-json <timing_metrics_json_file>]
[--make-runxml]
[--make-expxml]
[--force-copy]
[--skip-validate]
[--skip-upload]
[--test]\n";
}
GetOptions(
"metadata-urls=s" => \$metadata_url,
"vcfs=s" => \$vcfs,
"vcf-md5sum-files=s" => \$md5_file,
"vcf-idxs=s" => \$vcfs_idx,
"vcf-idx-md5sum-files=s" => \$md5_idx_file,
"tarballs=s" => \$tarballs,
"tarball-md5sum-files=s" => \$md5_tarball_file,
"outdir=s" => \$output_dir,
"key=s" => \$key,
"upload-url=s" => \$upload_url,
"workflow-src-url=s" => \$workflow_src_url,
"workflow-url=s" => \$workflow_url,
"workflow-name=s" => \$workflow_name,
"workflow-version=s" => \$workflow_version,
"seqware-version=s" => \$seqware_version,
"description-file=s" => \$description_file,
"study-refname-override=s" => \$study_ref_name,
"analysis-center-override=s" => \$analysis_center,
"pipeline-json=s" => \$pipeline_json_file,
"qc-metrics-json=s" => \$qc_json_file,
"timing-metrics-json=s" => \$timing_json_file,
"make-runxml" => \$make_runxml,
"make-expxml" => \$make_expxml,
"force-copy" => \$force_copy,
"skip-validate" => \$skip_validate,
"skip-upload" => \$skip_upload,
"test" => \$test,
);
##############
# MAIN STEPS #
##############
# setup output dir
say "SETTING UP OUTPUT DIR";
my $uuid = '';
my $ug = Data::UUID->new;
if(-d "$output_dir") {
opendir( my $dh, $output_dir);
my @dirs = grep {-d "$output_dir/$_" && ! /^\.{1,2}$/} readdir($dh);
if (scalar @dirs == 1) {
$uuid = $dirs[0];
}
else {
$uuid = lc($ug->create_str());
}
}
else {
$uuid = lc($ug->create_str());
}
$output_dir = "vcf/$output_dir";
run("mkdir -p $output_dir/$uuid");
$output_dir = "$output_dir/$uuid/";
my $final_touch_file = $output_dir."upload_complete.txt";
# parse values
my @vcf_arr = split /,/, $vcfs;
my @md5_file_arr = split /,/, $md5_file;
my @vcf_types_arr = split /,/, $vcf_types;
my @vcfs_idx_arr = split /,/, $vcfs_idx;
my @md5_idx_file_arr = split /,/, $md5_idx_file;
my @vcf_checksums;
my @idx_checksums;
my @tarball_checksums;
my @tarball_arr = split /,/, $tarballs;
my @md5_tarball_file_arr = split /,/, $md5_tarball_file;
# TODO: Sheldon, we'll need more validation here, check each VCF file for headers etc. See https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+VCF+Submission+SOP+-+v1.0
say 'VALIDATING PARAMS';
die "VCF and VCF md5sum file count don't match!\n" if ( scalar(@vcf_arr) != scalar(@md5_file_arr) );
die "VCF and VCF index count don't match!\n" if ( scalar(@vcf_arr) != scalar(@vcfs_idx_arr) );
die "VCF index and VCF index md5sum count don't match!\n" if ( scalar(@vcf_arr) != scalar(@md5_idx_file_arr) );
die "Tarball and Tarball md5sum count don't match!\n" if ( scalar(@tarball_arr) != scalar(@md5_tarball_file_arr) );
say 'COPYING FILES TO OUTPUT DIR';
my $link_method = ($force_copy)? 'rsync -rauv': 'ln -s';
my $pwd = `pwd`;
chomp $pwd;
for ( my $i = 0 ; $i < scalar(@vcf_arr) ; $i++ ) {
my $vcf_check = `cat $md5_file_arr[$i]`;
say "CAT CODE! cat $md5_file_arr[$i]";
my $idx_check = `cat $md5_idx_file_arr[$i]`;
chomp $vcf_check;
chomp $idx_check;
push @vcf_checksums, $vcf_check;
push @idx_checksums, $idx_check;
my @files = ($vcf_arr[$i], $md5_file_arr[$i], $vcfs_idx_arr[$i], $md5_idx_file_arr[$i]);
foreach my $file (@files) {
my $command = "$link_method $pwd/$file $output_dir/";
run($command) if (not (-e "$pwd/$output_dir/$file"));
}
}
for ( my $i = 0 ; $i < scalar(@tarball_arr) ; $i++ ) {
my $tarball_check = `cat $md5_tarball_file_arr[$i]`;
chomp $tarball_check;
push @tarball_checksums, $tarball_check;
run("$link_method $pwd/$tarball_arr[$i] $output_dir/");
}
say 'DOWNLOADING METADATA FILES';
my $metad = download_metadata($metadata_url);
my $input_json_hash = generate_input_json($metad);
my $output_json_hash = generate_output_json($metad);
say 'GENERATING SUBMISSION';
my $sub_path = generate_submission( $metad, $input_json_hash, $output_json_hash );
say 'VALIDATING SUBMISSION';
die "The submission did not pass validation! Files are located at: $sub_path\n"
if ( validate_submission($sub_path) );
say 'UPLOADING SUBMISSION';
die "The upload of files did not work! Files are located at: $sub_path\n"
if ( upload_submission($sub_path) );
###############
# SUBROUTINES #
###############
# this method generates a nice summary of the inputs to this workflow
# for inclusion in the analysis.xml
sub generate_input_json {
my ($metad) = @_;
my $d = {};
# cleanup and pull out the info I want, key off of specimen ID e.g. the SM field in the BAM header aka the aliquot_id in SRA XML
foreach my $url ( keys %{$metad} ) {
say "URL: $url";
# pull back the target sample UUID
my $target = $metad->{$url}{'target'}[0]{'refname'};
# now fill in various info
my $r = {};
$r->{'specimen'} = $target;
$r->{'attributes'}{'center_name'} = $metad->{$url}{'center_name'};
$r->{'attributes'}{'analysis_id'} = $metad->{$url}{'analysis_id'};
$r->{'attributes'}{'analysis_url'} = $url;
$r->{'attributes'}{'study_ref'} = $metad->{$url}{'study_ref'}[0]{'refname'};
$r->{'attributes'}{'dcc_project_code'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'dcc_project_code'} } );
$r->{'attributes'}{'submitter_donor_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_donor_id'} } );
$r->{'attributes'}{'submitter_sample_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_sample_id'} } );
$r->{'attributes'}{'dcc_specimen_type'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'dcc_specimen_type'} } );
$r->{'attributes'}{'use_cntl'} =
join( ",", keys %{ $metad->{$url}{'analysis_attr'}{'use_cntl'} } );
$r->{'attributes'}{'submitter_specimen_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_specimen_id'} }
);
push( @{ $d->{'workflow_inputs'} }, $r );
}
return $d;
}
# this method generates a nice summary of the outputs from this workflow
# for inclusion in the analysis.xml
sub generate_output_json {
my ($metad) = @_;
my $d = {};
# cleanup and pull out the info I want, key off of specimen ID e.g. the SM field in the BAM header aka the aliquot_id in SRA XML
foreach my $url ( keys %{$metad} ) {
say "URL: $url";
# pull back the target sample UUID
my $target = $metad->{$url}{'target'}[0]{'refname'};
# now fill in various info
my $r = {};
$r->{'specimen'} = $target;
$r->{'attributes'}{'center_name'} = $metad->{$url}{'center_name'};
$r->{'attributes'}{'analysis_id'} = $metad->{$url}{'analysis_id'};
$r->{'attributes'}{'analysis_url'} = $url;
$r->{'attributes'}{'study_ref'} =
$metad->{$url}{'study_ref'}[0]{'refname'};
$r->{'attributes'}{'dcc_project_code'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'dcc_project_code'} } );
$r->{'attributes'}{'submitter_donor_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_donor_id'} } );
$r->{'attributes'}{'submitter_sample_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_sample_id'} } );
$r->{'attributes'}{'dcc_specimen_type'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'dcc_specimen_type'} } );
$r->{'attributes'}{'use_cntl'} =
join( ",", keys %{ $metad->{$url}{'analysis_attr'}{'use_cntl'} } );
$r->{'attributes'}{'submitter_specimen_id'} = join( ',',
keys %{ $metad->{$url}{'analysis_attr'}{'submitter_specimen_id'} }
);
# now files
process_files( $r, $target, \@vcf_arr );
process_files( $r, $target, \@vcfs_idx_arr );
process_files( $r, $target, \@tarball_arr );
push( @{ $d->{'workflow_outputs'} }, $r );
}
return $d;
}
# parse info from the file name
# TODO: Sheldon, want better validation here... something that barfs if extra files are provided that don't conform to the naming standard. See https://wiki.oicr.on.ca/display/PANCANCER/PCAWG+VCF+Submission+SOP+-+v1.0
sub process_files {
my ( $r, $target, $arr ) = @_;
foreach my $file ( @{$arr} ) {
if ( $file =~ /$target\.([^\.]+)_([^\.]+)\.(\d+)\.([^\.]+)\./ ) {
$r->{'files'}{$file}{'specimen'} = $target;
$r->{'files'}{$file}{'workflow_name'} = $1;
my $workflow_version = $2;
$r->{'files'}{$file}{'date'} = $3;
$r->{'files'}{$file}{'file_type'} = $4;
$workflow_version =~ s/-/\./g;
$r->{'files'}{$file}{'workflow_version'} = $workflow_version;
}
}
return $r;
}
sub validate_submission {
my ( $sub_path, $vcf_check ) = @_;
my $cmd = "cgsubmit --validate-only -s $upload_url -o validation.log -u $sub_path -vv";
say "VALIDATING: $cmd";
unless ( $skip_validate ) {
die "ABORT: No cgsubmit installed, aborting!" if ( system("which cgsubmit") );
return run($cmd);
}
}
# TODO: need to standardize on the return values... 1 or 0!!
sub upload_submission {
my ($sub_path) = @_;
my $cmd = "cgsubmit -s $upload_url -o metadata_upload.log -u $sub_path -vv -c $key";
say "UPLOADING METADATA: $cmd";
if ( not $test && not $skip_upload ) {
croak "ABORT: No cgsubmit installed, aborting!" if( system("which cgsubmit"));
return 1 if ( run($cmd) );
}
# we need to hack the manifest.xml to drop any files that are inputs and I won't upload again
modify_manifest_file( "$sub_path/manifest.xml", $sub_path ) unless ($test);
my $log_file = 'upload.log';
my $gt_upload_command = "cd $sub_path; gtupload -v -c $key -l ./$log_file -u ./manifest.xml; cd -";
say "UPLOADING DATA: $cmd";
unless ( $test ) {
die "ABORT: No gtupload installed, aborting!" if ( system("which gtupload") );
return 1 if ( GNOS::Upload->run_upload($gt_upload_command, "$sub_path/$log_file", $retries, $cooldown, $md5_sleep) );
}
# just touch this file to ensure monitoring tools know upload is complete
run("date +\%s > $final_touch_file", "metadata_upload.log");
return 0;
}
sub modify_manifest_file {
my ( $man, $sub_path ) = @_;
open my $out, '>', "$man.new";
open my $in, '<', $man;
while (<$in>) {
chomp;
if (/filename="([^"]+)"/) {
if ( -e "$sub_path/$1" ) {
say $out $_;
}
}
else {
say $out $_;
}
}
close $in;
close $out;
system("mv $man.new $man");
return 1;
}
sub generate_submission {
my ( $m, $input_json_hash, $output_json_hash ) = @_;
# const
my $t = gmtime;
my $datetime = $t->datetime();
# populate refcenter from original BAM submission
# @RG CN:(.*)
my $refcenter = "OICR";
# @CO sample_id
my $sample_id = "";
# capture list
my $sample_uuids = {};
# current sample_uuid (which seems to actually be aliquot ID, this is sample ID from the BAM header)
my $sample_uuid = "";
# @RG SM or @CO aliquoit_id
my $aliquot_id = "";
# @RG LB:(.*)
my $library = "";
# @RG ID:(.*)
my $read_group_id = "";
# @RG PU:(.*)
my $platform_unit = "";
# @CO participant_id
my $participant_id = "";
# hardcoded
my $bam_file = "";
# hardcoded
my $bam_file_checksum = "";
# center name
my $center_name = "";
# these data are collected from all files
# aliquot_id|library_id|platform_unit|read_group_id|input_url
my $global_attr = {};
# input info
my $pi2 = {};
# this isn't going to work if there are multiple files/readgroups!
foreach my $file ( keys %{$m} ) {
# populate refcenter from original BAM submission
# @RG CN:(.*)
$refcenter = $m->{$file}{'target'}[0]{'refcenter'};
$center_name = $m->{$file}{'center_name'};
$sample_uuid = $m->{$file}{'target'}[0]{'refname'};
$sample_uuids->{ $m->{$file}{'target'}[0]{'refname'} } = 1;
# @CO sample_id
my @sample_ids = keys %{ $m->{$file}{'analysis_attr'}{'sample_id'} };
# workaround for updated XML
if ( scalar(@sample_ids) == 0 ) {
@sample_ids =
keys %{ $m->{$file}{'analysis_attr'}{'submitter_specimen_id'} };
}
$sample_id = $sample_ids[0];
# @RG SM or @CO aliquoit_id
my @aliquot_ids = keys %{ $m->{$file}{'analysis_attr'}{'aliquot_id'} };
# workaround for updated XML
if ( scalar(@aliquot_ids) == 0 ) {
@aliquot_ids =
keys %{ $m->{$file}{'analysis_attr'}{'submitter_sample_id'} };
}
$aliquot_id = $aliquot_ids[0];
# @RG LB:(.*)
$library = $m->{$file}{'run'}[0]{'data_block_name'};
# @RG ID:(.*)
$read_group_id = $m->{$file}{'run'}[0]{'read_group_label'};
# @RG PU:(.*)
$platform_unit = $m->{$file}{'run'}[0]{'refname'};
# @CO participant_id
my @participant_ids =
keys %{ $m->{$file}{'analysis_attr'}{'participant_id'} };
if ( scalar(@participant_ids) == 0 ) {
@participant_ids =
keys %{ $m->{$file}{'analysis_attr'}{'submitter_donor_id'} };
}
$participant_id = $participant_ids[0];
my $index = 0;
foreach my $bam_info ( @{ $m->{$file}{'run'} } ) {
if ( $bam_info->{data_block_name} ne '' ) {
my $pi = {};
$pi->{'input_info'}{'donor_id'} = $participant_id;
$pi->{'input_info'}{'specimen_id'} = $sample_id;
$pi->{'input_info'}{'target_sample_refname'} = $sample_uuid;
$pi->{'input_info'}{'analyzed_sample'} = $aliquot_id;
$pi->{'input_info'}{'library'} = $library;
$pi->{'input_info'}{'platform_unit'} = $platform_unit;
$pi->{'read_group_id'} = $read_group_id;
$pi->{'input_info'}{'analysis_id'} = $m->{$file}{'analysis_id'};
$pi->{'input_info'}{'bam_file'} =
$m->{$file}{'file'}[$index]{filename};
push @{ $pi2->{'pipeline_input_info'} }, $pi;
}
$index++;
}
# now combine the analysis attr
foreach my $attName ( keys %{ $m->{$file}{analysis_attr} } ) {
foreach
my $attVal ( keys %{ $m->{$file}{analysis_attr}{$attName} } )
{
$global_attr->{$attName}{$attVal} = 1;
}
}
}
my $str = to_json($pi2);
$global_attr->{"pipeline_input_info"}{$str} = 1;
my $description =
"This is the variant calling for specimen $sample_id from donor $participant_id. The results consist of one or more VCF files plus optional tar.gz files that contain additional file types. This uses the $workflow_name workflow, version $workflow_version available at $workflow_url. This workflow can be created from source, see $workflow_src_url. For a complete change log see $changelog_url. Note the 'ANALYSIS_TYPE' is 'REFERENCE_ASSEMBLY' but a better term to describe this analysis is 'SEQUENCE_VARIATION' as defined by the EGA's SRA 1.5 schema. Please note the reference used for alignment was hs37d, see ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707 for more information. Briefly this is the integrated reference sequence from the GRCh37 primary assembly (chromosomal plus unlocalized and unplaced contigs), the rCRS mitochondrial sequence (AC:NC_012920), Human herpesvirus 4 type 1 (AC:NC_007605) and the concatenated decoy sequences (hs37d5cs.fa.gz). Variant calls may not be present for all contigs in this reference.";
if ( $description_file ne "" && -e $description_file ) {
local $/ = undef;
open my $fh, '<', $description_file;
binmode $fh;
$description = <$fh>;
close $fh;
}
my $analysis_xml = <<END;
<ANALYSIS_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.analysis.xsd?view=co">
<ANALYSIS center_name="$center_name" analysis_center="$analysis_center" analysis_date="$datetime">
<TITLE>TCGA/ICGC PanCancer Donor-Level Variant Calling for Participant $participant_id</TITLE>
<STUDY_REF refcenter="$refcenter" refname="$study_ref_name" />
<DESCRIPTION>$description</DESCRIPTION>
<ANALYSIS_TYPE>
<REFERENCE_ALIGNMENT>
<ASSEMBLY>
<STANDARD short_name="GRCh37"/>
</ASSEMBLY>
<RUN_LABELS>
END
foreach my $url ( keys %{$m} ) {
foreach my $run ( @{ $m->{$url}{'run'} } ) {
if ( defined( $run->{'read_group_label'} ) ) {
my $dbn = $run->{'data_block_name'};
my $rgl = $run->{'read_group_label'};
my $rn = $run->{'refname'};
$analysis_xml .=
" <RUN data_block_name=\"$dbn\" read_group_label=\"$rgl\" refname=\"$rn\" refcenter=\"$center_name\" />\n";
}
}
}
$analysis_xml .= <<END;
</RUN_LABELS>
<SEQ_LABELS>
END
my $last_dbn = "";
foreach my $dbn ( keys %{$sample_uuids} ) {
$last_dbn = $dbn;
$analysis_xml .= <<END;
<SEQUENCE data_block_name="$dbn" accession="NC_000001.10" seq_label="1" />
<SEQUENCE data_block_name="$dbn" accession="NC_000002.11" seq_label="2" />
<SEQUENCE data_block_name="$dbn" accession="NC_000003.11" seq_label="3" />
<SEQUENCE data_block_name="$dbn" accession="NC_000004.11" seq_label="4" />
<SEQUENCE data_block_name="$dbn" accession="NC_000005.9" seq_label="5" />
<SEQUENCE data_block_name="$dbn" accession="NC_000006.11" seq_label="6" />
<SEQUENCE data_block_name="$dbn" accession="NC_000007.13" seq_label="7" />
<SEQUENCE data_block_name="$dbn" accession="NC_000008.10" seq_label="8" />
<SEQUENCE data_block_name="$dbn" accession="NC_000009.11" seq_label="9" />
<SEQUENCE data_block_name="$dbn" accession="NC_000010.10" seq_label="10" />
<SEQUENCE data_block_name="$dbn" accession="NC_000011.9" seq_label="11" />
<SEQUENCE data_block_name="$dbn" accession="NC_000012.11" seq_label="12" />
<SEQUENCE data_block_name="$dbn" accession="NC_000013.10" seq_label="13" />
<SEQUENCE data_block_name="$dbn" accession="NC_000014.8" seq_label="14" />
<SEQUENCE data_block_name="$dbn" accession="NC_000015.9" seq_label="15" />
<SEQUENCE data_block_name="$dbn" accession="NC_000016.9" seq_label="16" />
<SEQUENCE data_block_name="$dbn" accession="NC_000017.10" seq_label="17" />
<SEQUENCE data_block_name="$dbn" accession="NC_000018.9" seq_label="18" />
<SEQUENCE data_block_name="$dbn" accession="NC_000019.9" seq_label="19" />
<SEQUENCE data_block_name="$dbn" accession="NC_000020.10" seq_label="20" />
<SEQUENCE data_block_name="$dbn" accession="NC_000021.8" seq_label="21" />
<SEQUENCE data_block_name="$dbn" accession="NC_000022.10" seq_label="22" />
<SEQUENCE data_block_name="$dbn" accession="NC_000023.10" seq_label="X" />
<SEQUENCE data_block_name="$dbn" accession="NC_000024.9" seq_label="Y" />
<SEQUENCE data_block_name="$dbn" accession="NC_012920" seq_label="MT" />
<SEQUENCE data_block_name="$dbn" accession="GL000207.1" seq_label="GL000207.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000226.1" seq_label="GL000226.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000229.1" seq_label="GL000229.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000231.1" seq_label="GL000231.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000210.1" seq_label="GL000210.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000239.1" seq_label="GL000239.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000235.1" seq_label="GL000235.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000201.1" seq_label="GL000201.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000247.1" seq_label="GL000247.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000245.1" seq_label="GL000245.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000197.1" seq_label="GL000197.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000203.1" seq_label="GL000203.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000246.1" seq_label="GL000246.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000249.1" seq_label="GL000249.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000196.1" seq_label="GL000196.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000248.1" seq_label="GL000248.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000244.1" seq_label="GL000244.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000238.1" seq_label="GL000238.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000202.1" seq_label="GL000202.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000234.1" seq_label="GL000234.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000232.1" seq_label="GL000232.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000206.1" seq_label="GL000206.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000240.1" seq_label="GL000240.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000236.1" seq_label="GL000236.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000241.1" seq_label="GL000241.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000243.1" seq_label="GL000243.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000242.1" seq_label="GL000242.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000230.1" seq_label="GL000230.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000237.1" seq_label="GL000237.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000233.1" seq_label="GL000233.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000204.1" seq_label="GL000204.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000198.1" seq_label="GL000198.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000208.1" seq_label="GL000208.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000191.1" seq_label="GL000191.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000227.1" seq_label="GL000227.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000228.1" seq_label="GL000228.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000214.1" seq_label="GL000214.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000221.1" seq_label="GL000221.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000209.1" seq_label="GL000209.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000218.1" seq_label="GL000218.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000220.1" seq_label="GL000220.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000213.1" seq_label="GL000213.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000211.1" seq_label="GL000211.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000199.1" seq_label="GL000199.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000217.1" seq_label="GL000217.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000216.1" seq_label="GL000216.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000215.1" seq_label="GL000215.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000205.1" seq_label="GL000205.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000219.1" seq_label="GL000219.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000224.1" seq_label="GL000224.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000223.1" seq_label="GL000223.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000195.1" seq_label="GL000195.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000212.1" seq_label="GL000212.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000222.1" seq_label="GL000222.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000200.1" seq_label="GL000200.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000193.1" seq_label="GL000193.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000194.1" seq_label="GL000194.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000225.1" seq_label="GL000225.1" />
<SEQUENCE data_block_name="$dbn" accession="GL000192.1" seq_label="GL000192.1" />
<SEQUENCE data_block_name="$dbn" accession="NC_007605" seq_label="NC_007605" />
<SEQUENCE data_block_name="$dbn" accession="hs37d5" seq_label="hs37d5" />
END
}
$analysis_xml .= <<END;
</SEQ_LABELS>
<PROCESSING>
<PIPELINE>
END
if ( $pipeline_json_file ne "" && -e $pipeline_json_file ) {
local $/ = undef;
open my $fh, '<', $pipeline_json_file;
binmode $fh;
my $json = <$fh>;
close $fh;
my $d = decode_json($json);
foreach my $r ( @{ $d->{'pipe'} } ) {
my $section_name = $r->{'section_name'};
my $step_index = $r->{'step_index'};
my $previous_step_index = $r->{'previous_step_index'};
my $program = $r->{'program'};
my $version = $r->{'version'};
my $notes = $r->{'notes'};
$analysis_xml .= <<END;
<PIPE_SECTION section_name="$section_name">
<STEP_INDEX>$step_index</STEP_INDEX>
<PREV_STEP_INDEX>$previous_step_index</PREV_STEP_INDEX>
<PROGRAM>$program</PROGRAM>
<VERSION>$version</VERSION>
<NOTES>$notes</NOTES>
</PIPE_SECTION>
END
}
}
else {
$analysis_xml .= <<END;
<PIPE_SECTION section_name="SeqWare_$seqware_version">
<STEP_INDEX>1</STEP_INDEX>
<PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
<PROGRAM>$workflow_name</PROGRAM>
<VERSION>$workflow_version</VERSION>
<NOTES></NOTES>
</PIPE_SECTION>
END
}
$analysis_xml .= <<END;
</PIPELINE>
<DIRECTIVES>
<alignment_includes_unaligned_reads>true</alignment_includes_unaligned_reads>
<alignment_marks_duplicate_reads>true</alignment_marks_duplicate_reads>
<alignment_includes_failed_reads>false</alignment_includes_failed_reads>
</DIRECTIVES>
</PROCESSING>
</REFERENCE_ALIGNMENT>
</ANALYSIS_TYPE>
<TARGETS>
END
foreach my $curr_sample_uuid ( keys %{$sample_uuids} ) {
$analysis_xml .= <<END;
<TARGET sra_object_type="SAMPLE" refcenter="$refcenter" refname="$curr_sample_uuid" />
END
}
$analysis_xml .= <<END;
</TARGETS>
<DATA_BLOCK name=\"$last_dbn\">
<FILES>
END
# VCF files
for ( my $i = 0 ; $i < scalar(@vcf_arr) ; $i++ ) {
$vcf_arr[$i] =~ /^\S*\/([^\/]+)$/;
my $curr_vcf = $1;
$vcfs_idx_arr[$i] =~ /^\S*\/([^\/]+)$/;
my $curr_index = $1;
$analysis_xml .=
" <FILE filename=\"$curr_vcf\" filetype=\"vcf\" checksum_method=\"MD5\" checksum=\"$vcf_checksums[$i]\" />\n";
$analysis_xml .=
" <FILE filename=\"$curr_index\" filetype=\"idx\" checksum_method=\"MD5\" checksum=\"$idx_checksums[$i]\" />\n";
}
# Tarball files
for ( my $i = 0 ; $i < scalar(@tarball_arr) ; $i++ ) {
$tarball_arr[$i] =~ /^\S*\/([^\/]+)$/;
my $curr_tar = $1;
$analysis_xml .=
" <FILE filename=\"$curr_tar\" filetype=\"tar\" checksum_method=\"MD5\" checksum=\"$tarball_checksums[$i]\" />\n";
}
$analysis_xml .= <<END;
</FILES>
</DATA_BLOCK>
<ANALYSIS_ATTRIBUTES>
END
# this is a merge of the key-values from input XML
# changing some key names to prevent conflicts
# I'm actually now skipping a lot more than before since 1) combining multiple inputs makes this more complex, 2) I have a nice JSON that describes inputs/outputs and 3) folks can look back at the original BAM analysis.xml for more details if they need it, no need to duplicate here.
foreach my $key ( keys %{$global_attr} ) {
foreach my $val ( keys %{ $global_attr->{$key} } ) {
if ( $key eq "pipeline_input_info" ) {
#$key = "alignment_pipeline_input_info";
next;
}
elsif ( $key eq "workflow_name" ) {
$key = "alignment_workflow_name";
}
elsif ( $key eq "workflow_version" ) {
$key = "alignment_workflow_version";
}
elsif ( $key eq "workflow_source_url" ) {
$key = "alignment_workflow_source_url";
}
elsif ( $key eq "workflow_bundle_url" ) {
$key = "alignment_workflow_bundle_url";
}
elsif ( $key eq "workflow_output_bam_contents" ) {
#$key = "alignment_workflow_output_bam_contents";
next;
}
elsif ( $key eq "qc_metrics" ) {
#$key = "alignment_qc_metrics";
next;
}
elsif ( $key eq "timing_metrics" ) {
#$key = "alignment_timing_metrics";
next;
}
elsif ( $key eq "markduplicates_metrics" ) {
#$key = "alignment_markduplicates_metrics";
next;
}
elsif ( $key eq "bwa_version" ) {
#$key = "alignment_bwa_version";
next;
}
elsif ( $key eq "biobambam_version" ) {
#$key = "alignment_biobambam_version";
next;
}
elsif ( $key eq "PCAP-core_version" ) {
#$key = "alignment_PCAP-core_version";
next;
}
elsif ($key eq "total_lanes"
|| $key eq "dcc_specimen_type"
|| $key eq "use_cntl"
|| $key eq "submitter_specimen_id"
|| $key eq "submitter_sample_id" )
{
#$key = "alignment_PCAP-core_version";
next;
}
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>$key</TAG>
<VALUE>$val</VALUE>
</ANALYSIS_ATTRIBUTE>
";
}
}
# TODO
# variant_pipeline_input_info
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>variant_pipeline_input_info</TAG>
<VALUE>" . &to_json($input_json_hash) . "</VALUE>
</ANALYSIS_ATTRIBUTE>
";
# TODO
# variant_pipeline_output_info
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>variant_pipeline_output_info</TAG>
<VALUE>" . &to_json($output_json_hash) . "</VALUE>
</ANALYSIS_ATTRIBUTE>
";
# some metadata about this workflow
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>variant_workflow_name</TAG>
<VALUE>$workflow_name</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>variant_workflow_version</TAG>
<VALUE>$workflow_version</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>variant_workflow_source_url</TAG>
<VALUE>$workflow_src_url</VALUE>
</ANALYSIS_ATTRIBUTE>
<ANALYSIS_ATTRIBUTE>
<TAG>variant_workflow_bundle_url</TAG>
<VALUE>$workflow_url</VALUE>
</ANALYSIS_ATTRIBUTE>
";
# TODO QC
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>variant_qc_metrics</TAG>
<VALUE>" . &getQcResult() . "</VALUE>
</ANALYSIS_ATTRIBUTE>
";
# TODO Runtime
$analysis_xml .= " <ANALYSIS_ATTRIBUTE>
<TAG>variant_timing_metrics</TAG>
<VALUE>" . &getRuntimeInfo() . "</VALUE>
</ANALYSIS_ATTRIBUTE>
";
$analysis_xml .= <<END;
</ANALYSIS_ATTRIBUTES>
</ANALYSIS>
</ANALYSIS_SET>
END
open my $out, '>', "$output_dir/analysis.xml";
print $out $analysis_xml;
close $out;
# make a uniq list of blocks
my $uniq_exp_xml = {};
foreach my $url ( keys %{$m} ) {
$uniq_exp_xml->{ $m->{$url}{'experiment'} } = 1;
}
my $exp_xml = <<END;
<EXPERIMENT_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.experiment.xsd?view=co">
END
foreach my $curr_xml_block ( keys %{$uniq_exp_xml} ) {
$exp_xml .= $curr_xml_block;
}
$exp_xml .= <<END;
</EXPERIMENT_SET>
END
if ($make_expxml) {
open my $out, '>', "$output_dir/experiment.xml";
say $out $exp_xml;
close $out;
}
# make a uniq list of blocks
my $uniq_run_xml = {};
foreach my $url ( keys %{$m} ) {
my $run_block = $m->{$url}{'run_block'};
# no longer modifying the run block, this is the original input reads *not* the aligned BAM result!
#$run_block =~ s/filename="\S+"/filename="$bam_check.bam"/g;
#$run_block =~ s/checksum="\S+"/checksum="$bam_check"/g;
#$run_block =~ s/center_name="[^"]+"/center_name="$refcenter"/g;
$uniq_run_xml->{$run_block} = 1;
}
my $run_xml = <<END;
<RUN_SET xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.run.xsd?view=co">
END
foreach my $run_block ( keys %{$uniq_run_xml} ) {
$run_xml .= $run_block;
}
$run_xml .= <<END;
</RUN_SET>
END
if ($make_runxml) {
open my $out, '>', "$output_dir/run.xml";
print $out $run_xml;
close $out;
}
return ($output_dir);
}
sub read_header {
my ($header) = @_;
my $hd = {};
open my $header_fh, '<', $header;
while (<$header_fh>) {
chomp;
my @a = split /\t+/;
my $type = $a[0];
if ( $type =~ /^@/ ) {
$type =~ s/@//;
for ( my $i = 1 ; $i < scalar(@a) ; $i++ ) {
$a[$i] =~ /^([^:]+):(.+)$/;
$hd->{$type}{$1} = $2;
}
}
}
close $header_fh;
return $hd;
}