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Merge pull request #867 from mgcam/lane_level_review
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Simpifies autoqc function code and allows for lane-level review autoqc
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@marcomoscasgr
marcomoscasgr authored Nov 19, 2024
2 parents 7f27799 + ea3a4d0 commit dbbb6e8
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Showing 6 changed files with 163 additions and 151 deletions.
5 changes: 5 additions & 0 deletions Changes
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@@ -1,6 +1,11 @@
LIST OF CHANGES
---------------

- npg_pipeline::function::autoqc
- Simplified the flow of the code.
- Made clearer logic for choosing QC checks to run, provided comments.
- Allowed for running the review QC check on lanes.

release 68.6.0 (2024-10-24)
- The runfolder_path attribute is passed to the constructor of the review
autoqc check object when deciding whether this check should run.
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1 change: 1 addition & 0 deletions MANIFEST
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Original file line number Diff line number Diff line change
Expand Up @@ -1042,6 +1042,7 @@ t/data/release/config/notify_off/product_release.yml
t/data/release/config/notify_on/product_release.yml
t/data/release/config/qc_review/product_release.yml
t/data/release/config/qc_review_default/product_release.yml
t/data/release/config/qc_review_default_with_lane/product_release.yml
t/data/release/config/pp_archival/product_release.yml
t/data/release/config/pp_archival/product_release_no_array.yml
t/data/release/config/pp_archival/product_release_no_filters.yml
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193 changes: 77 additions & 116 deletions lib/npg_pipeline/function/autoqc.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,23 @@ with q{npg_pipeline::function::util};

our $VERSION = '0';

Readonly::Scalar my $QC_SCRIPT_NAME => q{qc};
Readonly::Scalar my $QC_SCRIPT_NAME => q{qc};

Readonly::Array my @CHECKS_NEED_PAIREDNESS_INFO => qw/
insert_size
gc_fraction
qX_yield
/;

Readonly::Scalar my $TARGET_FILE_CHECK_RE => qr{ \A
adapter |
bcfstats |
verify_bam_id |
genotype |
pulldown_metrics |
haplotag_metrics
\Z }xms;

has q{qc_to_run} => (isa => q{Str},
is => q{ro},
required => 1,);
Expand All @@ -51,47 +61,6 @@ sub _build__check_uses_refrepos {
->find_attribute_by_name('repository') ? 1 : 0;
}

has q{_is_lane_level_check} => (
isa => q{Bool},
is => q{ro},
required => 0,
init_arg => undef,
lazy_build => 1,);
sub _build__is_lane_level_check {
my $self = shift;
return $self->qc_to_run() =~ /^ spatial_filter $/smx;
}

has q{_is_lane_level_check4indexed_lane} => (
isa => q{Bool},
is => q{ro},
required => 0,
init_arg => undef,
lazy_build => 1,);
sub _build__is_lane_level_check4indexed_lane {
my $self = shift;
return $self->qc_to_run() =~ /^ tag_metrics $/smx;
}

has q{_is_check4target_file} => (
isa => q{Bool},
is => q{ro},
required => 0,
init_arg => undef,
lazy_build => 1,);
sub _build__is_check4target_file {
my $self = shift;
##no critic (RegularExpressions::RequireBracesForMultiline)
##no critic (RegularExpressions::ProhibitComplexRegexes)
return $self->qc_to_run() =~ /^ adapter |
bcfstats |
verify_bam_id |
genotype |
pulldown_metrics |
haplotag_metrics |
review $/smx;
}

sub BUILD {
my $self = shift;
load_class($self->_qc_module_name);
Expand All @@ -111,15 +80,19 @@ sub create {
push @definitions, $self->_create_definition4interop();
} else {

my $is_lane = 1;
for my $lp (@{$self->products->{lanes}}) {

$self->debug(sprintf ' autoqc check %s for lane, rpt_list: %s, is_pool: %s',
$self->qc_to_run(), $lp->rpt_list, ($lp->lims->is_pool? q[True]: q[False]));

$done_as_lane{$lp->rpt_list} = 1;
push @definitions, $self->_create_definition($lp, 0); # is_plex is always 0 here
if ($self->_should_run($lp, $is_lane)) {
push @definitions, $self->_create_definition($lp);
}
}

$is_lane = 0;
for my $dp (@{$self->products->{data_products}}) {
# skip data_products that have already been processed as lanes
# (i.e. libraries or single-sample pools)
Expand All @@ -133,7 +106,9 @@ sub create {
$self->qc_to_run(), $dp->{rpt_list}, ($is_plex? q[True]: q[False]),
($dp->lims->is_pool? q[True]: q[False]), ($is_plex? $tag_index: q[NONE]));

push @definitions, $self->_create_definition($dp, $is_plex);
if ($self->_should_run($dp, $is_lane, $is_plex)) {
push @definitions, $self->_create_definition($dp);
}
}
}

Expand All @@ -145,14 +120,17 @@ sub create {
}

sub _create_definition {
my ($self, $product, $is_plex) = @_;

if ($self->_should_run($is_plex, $product)) {
my $command = $self->_generate_command($product);
return $self->_create_definition_object($product, $command);
my ($self, $product) = @_;

my $ref = {
'job_name' => $self->_job_name(),
'composition' => $product->composition,
'command' => $self->_generate_command($product)
};
if ( ($self->qc_to_run eq 'adapter') || $self->_check_uses_refrepos() ) {
$ref->{'command_preexec'} = $self->repos_pre_exec_string();
}

return;
return $self->create_definition($ref);
}

sub _job_name {
Expand Down Expand Up @@ -190,23 +168,6 @@ sub _create_definition4interop {
return $self->create_definition($ref);
}

sub _create_definition_object {
my ($self, $product, $command) = @_;

my $ref = {};
my $qc_to_run = $self->qc_to_run;

$ref->{'job_name'} = $self->_job_name();
$ref->{'composition'} = $product->composition;
$ref->{'command'} = $command;

if ( ($qc_to_run eq 'adapter') || $self->_check_uses_refrepos() ) {
$ref->{'command_preexec'} = $self->repos_pre_exec_string();
}

return $self->create_definition($ref);
}

sub _generate_command {
my ($self, $dp) = @_;

Expand Down Expand Up @@ -282,64 +243,64 @@ sub _generate_command {
}

sub _should_run {
my ($self, $is_plex, $product) = @_;

my $can_run = 1;
my ($self, $product, $is_lane, $is_plex) = @_;

my $is_lane = !$is_plex; # if it's not a plex, it's a lane
my $rpt_list = $product->rpt_list;
my $is_pool = $product->lims->is_pool;
my $is_tag_zero = $product->is_tag_zero_product;
my $is_pool = $product->lims->is_pool; # Note - true for merged data.

if($self->qc_to_run() eq 'spatial_filter' and ($self->platform_NovaSeq or $self->platform_NovaSeqX)) {
return 0;
if ($self->qc_to_run() eq 'spatial_filter') {
# Run on individual lanes only.
return $is_lane && !($self->platform_NovaSeq || $self->platform_NovaSeqX) ? 1 : 0;
}

if ($self->_is_lane_level_check()) {
return !$is_plex;
if ($self->qc_to_run() eq 'tag_metrics') {
# For indexed runs, run on individual lanes if they are pools of samples.
return $self->is_indexed() && $is_lane && $is_pool ? 1 : 0;
}

if ($self->_is_lane_level_check4indexed_lane()) {
return $is_lane && $is_pool;
if ($self->qc_to_run() eq 'review') {
# This check should never run on tag zero, other entities are fair game.
if ($is_plex && $product->is_tag_zero_product) {
return 0;
}
}

if ($self->_is_check4target_file()) {
$can_run = (($is_lane && !$is_pool) ||
($is_plex && !$is_tag_zero));
if ($self->qc_to_run() =~ $TARGET_FILE_CHECK_RE) {
# Do not run on tag zero files, unmerged or merged.
# Do not run on lane-level data if the lane is a pool.
# Run on lane-level data for a single library.
# Run on merged plexes or lanes.
if (($is_plex && $product->is_tag_zero_product) || ($is_lane && $is_pool)) {
return 0;
}
}

if ($can_run) {
my %init_hash = ( rpt_list => $rpt_list, lims => $product->lims );

if ($self->has_repository && $self->_check_uses_refrepos()) {
$init_hash{'repository'} = $self->repository;
}
if ($self->qc_to_run() eq 'insert_size') {
$init_hash{'is_paired_read'} = $self->is_paired_read() ? 1 : 0;
} elsif ($self->qc_to_run() eq 'review') {
$init_hash{'product_conf_file_path'} = $self->product_conf_file_path;
$init_hash{'runfolder_path'} = $self->runfolder_path;
} elsif ($self->qc_to_run() eq 'genotype') {
my $ref_fasta = npg_pipeline::cache::reference->instance()
->get_path($product, q(fasta), $self->repository());
if ($ref_fasta) {
$init_hash{'reference_fasta'} = $ref_fasta;
}
# The rest will abide by the return value of the can_run method of the
# autoqc check. We have to provide enough argument to the constructor for
# the object to be created and can_run to execute.
my %init_hash = ( rpt_list => $product->rpt_list, lims => $product->lims );
if ($self->has_repository && $self->_check_uses_refrepos()) {
$init_hash{'repository'} = $self->repository;
}
if ($self->qc_to_run() eq 'insert_size') {
$init_hash{'is_paired_read'} = $self->is_paired_read() ? 1 : 0;
} elsif ($self->qc_to_run() eq 'review') {
$init_hash{'product_conf_file_path'} = $self->product_conf_file_path;
$init_hash{'runfolder_path'} = $self->runfolder_path;
} elsif ($self->qc_to_run() eq 'genotype') {
my $ref_fasta = npg_pipeline::cache::reference->instance()
->get_path($product, q(fasta), $self->repository());
if ($ref_fasta) {
$init_hash{'reference_fasta'} = $ref_fasta;
}

my $class = $self->_qc_module_name();
my $check_obj;
try {
$check_obj = $class->new(\%init_hash);
} catch {
delete $init_hash{'lims'};
$check_obj = $class->new(\%init_hash);
};

$can_run = $check_obj->can_run();
}

return $can_run;
my $class = $self->_qc_module_name();
my $check_obj;
try {
$check_obj = $class->new(\%init_hash);
} catch {
delete $init_hash{'lims'};
$check_obj = $class->new(\%init_hash); # Allow to fail at this stage.
};

return $check_obj->can_run();
}

__PACKAGE__->meta->make_immutable;
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