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Merge pull request #837 from mgcam/merge_exclude_option
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Added an option to exclude lanes from a merge.
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@dkj
dkj committed Apr 19, 2024
2 parents 48bf0a1 + 46d9e3f commit a246ae9
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Showing 2 changed files with 97 additions and 10 deletions.
54 changes: 46 additions & 8 deletions lib/npg_pipeline/base.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -187,7 +187,10 @@ sub _build_general_values_conf {
=head2 merge_lanes
Tells p4 stage2 (seq_alignment) to merge all lanes (at their plex level
if plexed) and to run its downstream tasks using corresponding compositions.
if plexed, except spiked PhiX and tag_zero).
If not set, this attribute is build lazily. It is set to true for NovaSeq runs,
which use a Standard flowcell.
=cut

Expand All @@ -208,6 +211,12 @@ sub _build_merge_lanes {

=head2 merge_by_library
Tells p4 stage2 (seq_alignment) to merge all plexes that belong to the same
library, except spiked PhiX and tag_zero.
If not set, this attribute is build lazily. It is set to true for indexed
NovaSeqX runs.
=cut

has q{merge_by_library} => (
Expand All @@ -216,13 +225,32 @@ has q{merge_by_library} => (
lazy_build => 1,
documentation => q{Tells p4 stage2 (seq_alignment) to merge all plexes } .
q{that belong to the same library, except spiked PhiX and }.
q{tag zero)},
q{tag zero},
);
sub _build_merge_by_library {
my $self = shift;
return $self->is_indexed && $self->platform_NovaSeqX();
}

=head2 process_separately_lanes
An array of lane (position) numbers, which should not be merged with anyother
lanes. To be used in conjunction with C<merge_lanes> or C<merge_by_library>
attributes. Does not have any impact if both of these attributes are false.
Defaults to an empty array value, meaning that all possible entities will be
merged.
=cut

has q{process_separately_lanes} => (
isa => q{ArrayRef},
is => q{ro},
default => sub { return []; },
documentation => q{Array of lane numbers, which have to be excluded from } .
q{a merge},
);

=head2 lims
st::api::lims run-level or product-specific object
Expand Down Expand Up @@ -346,7 +374,8 @@ sub _build_products {

if ($self->merge_lanes || $self->merge_by_library) {

my $all_lims = $self->lims->aggregate_libraries(\@lane_lims);
my $all_lims = $self->lims->aggregate_libraries(
\@lane_lims, $self->process_separately_lanes);
@data_lims = @{$all_lims->{'singles'}}; # Might be empty.

# merge_lanes option implies a merge across all lanes.
Expand Down Expand Up @@ -425,18 +454,27 @@ sub _lims_object2product {
sub _check_lane_merge_is_viable {
my ($self, $lane_lims, $singles, $merges) = @_;

my %no_merge_lanes = map { $_ => 1 } @{$self->process_separately_lanes};
my @num_plexes = uniq
map { scalar @{$_} }
map { [grep { !$_->is_control } @{$_}] }
map { [$_->children()] } @{$lane_lims};
map { scalar @{$_} }
map { [grep { !$_->is_control } @{$_}] }
map { [$_->children()] }
grep { ! exists $no_merge_lanes{$_->position} }
@{$lane_lims};

my $m = 'merge_lane option is not viable: ';
if (@num_plexes > 1) {
$self->logcroak($m . 'different number of samples in lanes');
}
if (any { !$_->is_control } @{$singles}) {
$self->logcroak($m . 'unmerged samples are present after aggregation');

my @unmerged_unexpected = grep { ! exists $no_merge_lanes{$_->position} }
grep { !$_->is_control }
@{$singles};
if (@unmerged_unexpected) {
$self->logcroak(
$m . 'unexpected unmerged samples are present after aggregation');
}

if (@{$merges} != $num_plexes[0]) {
$self->logcroak($m . 'number of merged samples after aggregation ' .
'differs from the number of samples in a lane');
Expand Down
53 changes: 51 additions & 2 deletions t/10-base.t
View file
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ subtest 'repository preexec' => sub {
};

subtest 'products - merging (or not) lanes' => sub {
plan tests => 19;
plan tests => 22;

my $rf_path = q[t/data/novaseqx/20231017_LH00210_0012_B22FCNFLT3];
my $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 47995);
Expand All @@ -79,12 +79,23 @@ subtest 'products - merging (or not) lanes' => sub {
cp 't/data/novaseq/210111_A00513_0447_AHJ55JDSXY/RunInfo.xml', "$rf_path/RunInfo.xml";
$b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 999);
ok ($b->merge_lanes, 'merge_lanes flag is set');
ok (!$b->_selected_lanes, 'selected_lanes flag is not set');
lives_ok {$products = $b->products} 'products hash created for NovaSeq run';
ok (exists $products->{'lanes'}, 'products lanes key exists');
is (scalar @{$products->{'lanes'}}, 4, 'four lane product');
ok (exists $products->{'data_products'}, 'products data_products key exists');
is (scalar @{$products->{'data_products'}}, 29, '29 data products');

$b = npg_pipeline::base->new(
runfolder_path => $rf_path,
id_run => 999,
merge_lanes => 1,
process_separately_lanes => [2]
);
# 8 products out of previous 29 are tag zero and spiked phiX
is (scalar @{$b->products->{'data_products'}}, 50, '50 data products');
ok ($b->_selected_lanes, 'selected_lanes flag is set');

local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_rapidrun_nopool.csv';
cp 't/data/run_params/runParameters.hiseq.rr.xml', "$rf_path/runParameters.xml";
cp 't/data/run_params/RunInfo.hiseq.rr.xml', "$rf_path/RunInfo.xml";
Expand All @@ -109,7 +120,7 @@ subtest 'products - merging (or not) lanes' => sub {
};

subtest 'products - merging (or not) libraries' => sub {
plan tests => 418;
plan tests => 423;

my $rf_info = $util->create_runfolder();
my $rf_path = $rf_info->{'runfolder_path'};
Expand Down Expand Up @@ -173,6 +184,22 @@ subtest 'products - merging (or not) libraries' => sub {
ok ($p->selected_lanes, 'selected_lanes flag is set to true');
}

$b = npg_pipeline::base->new(
runfolder_path => $rf_path,
id_run => $id_run,
process_separately_lanes => [1,2,5,6]
);
@products = @{$b->products()->{'data_products'}};
is (@products, 142, 'number of data products is 142');

$b = npg_pipeline::base->new(
runfolder_path => $rf_path,
id_run => $id_run,
process_separately_lanes => [1,6]
);
@products = @{$b->products()->{'data_products'}};
is (@products, 142, 'number of data products is 142');

# Expect lanes 3 and 4 merged.
$b = npg_pipeline::base->new(
runfolder_path => $rf_path, id_run => $id_run, lanes => [4,8,3]);
Expand Down Expand Up @@ -236,6 +263,28 @@ subtest 'products - merging (or not) libraries' => sub {
}
}
is (@products, 0, 'no products are left');

# remove lane 3 from the merge - no merge will take place
$b = npg_pipeline::base->new(
runfolder_path => $rf_path,
id_run => $id_run,
lanes => [4,8,3],
merge_by_library => 1,
process_separately_lanes => [3]
);
@products = @{$b->products()->{'data_products'}};
is (@products, 64, 'number of data products is 64');

$b = npg_pipeline::base->new(
runfolder_path => $rf_path,
id_run => $id_run,
lanes => [4,8,3],
merge_by_library => 0,
process_separately_lanes => [3,8]
);
lives_ok { @products = @{$b->products()->{'data_products'}} }
'process_separately_lanes is compatible with suppressed merge';
is (@products, 64, 'number of data products is 64');
};

sub _generate_rpt {
Expand Down

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