@@ -19,13 +19,23 @@ with q{npg_pipeline::function::util};
1919
2020our $VERSION = ' 0'
2121
22- Readonly::Scalar my $QC_SCRIPT_NAME => q{ qc}
22+ Readonly::Scalar my $QC_SCRIPT_NAME => q{ qc}
23+
2324Readonly::Array my @CHECKS_NEED_PAIREDNESS_INFO => qw/
2425 insert_size
2526 gc_fraction
2627 qX_yield
2728 / ;
2829
30+ Readonly::Scalar my $TARGET_FILE_CHECK_RE => qr {\A
31+ adapter |
32+ bcfstats |
33+ verify_bam_id |
34+ genotype |
35+ pulldown_metrics |
36+ haplotag_metrics
37+ \Z } xms
38+
2939has q{ qc_to_run} => (isa => q{ Str}
3040 is => q{ ro}
3141 required => 1,);
@@ -51,47 +61,6 @@ sub _build__check_uses_refrepos {
5161 -> find_attribute_by_name(' repository'
5262}
5363
54- has q{ _is_lane_level_check} => (
55- isa => q{ Bool}
56- is => q{ ro}
57- required => 0,
58- init_arg => undef ,
59- lazy_build => 1,);
60- sub _build__is_lane_level_check {
61- my $self = shift ;
62- return $self -> qc_to_run() =~ / ^ spatial_filter $ /smx
63- }
64-
65- has q{ _is_lane_level_check4indexed_lane} => (
66- isa => q{ Bool}
67- is => q{ ro}
68- required => 0,
69- init_arg => undef ,
70- lazy_build => 1,);
71- sub _build__is_lane_level_check4indexed_lane {
72- my $self = shift ;
73- return $self -> qc_to_run() =~ / ^ tag_metrics $ /smx
74- }
75-
76- has q{ _is_check4target_file} => (
77- isa => q{ Bool}
78- is => q{ ro}
79- required => 0,
80- init_arg => undef ,
81- lazy_build => 1,);
82- sub _build__is_check4target_file {
83- my $self = shift ;
84- # #no critic (RegularExpressions::RequireBracesForMultiline)
85- # #no critic (RegularExpressions::ProhibitComplexRegexes)
86- return $self -> qc_to_run() =~ / ^ adapter |
87- bcfstats |
88- verify_bam_id |
89- genotype |
90- pulldown_metrics |
91- haplotag_metrics |
92- review $ /smx ;
93- }
94-
9564sub BUILD {
9665 my $self = shift ;
9766 load_class($self -> _qc_module_name);
@@ -111,15 +80,19 @@ sub create {
11180 push @definitions , $self -> _create_definition4interop();
11281 } else {
11382
83+ my $is_lane = 1;
11484 for my $lp (@{$self -> products-> {lanes }}) {
11585
11686 $self -> debug(sprintf ' autoqc check %s for lane, rpt_list: %s, is_pool: %s'
11787 $self -> qc_to_run(), $lp -> rpt_list, ($lp -> lims-> is_pool? q[ True] q[ False]
11888
11989 $done_as_lane {$lp -> rpt_list} = 1;
120- push @definitions , $self -> _create_definition($lp , 0); # is_plex is always 0 here
90+ if ($self -> _should_run($lp , $is_lane )) {
91+ push @definitions , $self -> _create_definition($lp );
92+ }
12193 }
12294
95+ $is_lane = 0;
12396 for my $dp (@{$self -> products-> {data_products }}) {
12497 # skip data_products that have already been processed as lanes
12598 # (i.e. libraries or single-sample pools)
@@ -133,7 +106,9 @@ sub create {
133106 $self -> qc_to_run(), $dp -> {rpt_list }, ($is_plex ? q[ True] q[ False]
134107 ($dp -> lims-> is_pool? q[ True] q[ False] $is_plex ? $tag_index : q[ NONE]
135108
136- push @definitions , $self -> _create_definition($dp , $is_plex );
109+ if ($self -> _should_run($dp , $is_lane , $is_plex )) {
110+ push @definitions , $self -> _create_definition($dp );
111+ }
137112 }
138113 }
139114
@@ -145,14 +120,17 @@ sub create {
145120}
146121
147122sub _create_definition {
148- my ($self , $product , $is_plex ) = @_ ;
149-
150- if ($self -> _should_run($is_plex , $product )) {
151- my $command = $self -> _generate_command($product );
152- return $self -> _create_definition_object($product , $command );
123+ my ($self , $product ) = @_ ;
124+
125+ my $ref = {
126+ ' job_name' => $self -> _job_name(),
127+ ' composition' => $product -> composition,
128+ ' command' => $self -> _generate_command($product )
129+ };
130+ if ( ($self -> qc_to_run eq ' adapter' $self -> _check_uses_refrepos() ) {
131+ $ref -> {' command_preexec' $self -> repos_pre_exec_string();
153132 }
154-
155- return ;
133+ return $self -> create_definition($ref );
156134}
157135
158136sub _job_name {
@@ -190,23 +168,6 @@ sub _create_definition4interop {
190168 return $self -> create_definition($ref );
191169}
192170
193- sub _create_definition_object {
194- my ($self , $product , $command ) = @_ ;
195-
196- my $ref = {};
197- my $qc_to_run = $self -> qc_to_run;
198-
199- $ref -> {' job_name' $self -> _job_name();
200- $ref -> {' composition' $product -> composition;
201- $ref -> {' command' $command ;
202-
203- if ( ($qc_to_run eq ' adapter' $self -> _check_uses_refrepos() ) {
204- $ref -> {' command_preexec' $self -> repos_pre_exec_string();
205- }
206-
207- return $self -> create_definition($ref );
208- }
209-
210171sub _generate_command {
211172 my ($self , $dp ) = @_ ;
212173
@@ -282,64 +243,64 @@ sub _generate_command {
282243}
283244
284245sub _should_run {
285- my ($self , $is_plex , $product ) = @_ ;
286-
287- my $can_run = 1;
246+ my ($self , $product , $is_lane , $is_plex ) = @_ ;
288247
289- my $is_lane = !$is_plex ; # if it's not a plex, it's a lane
290- my $rpt_list = $product -> rpt_list;
291- my $is_pool = $product -> lims-> is_pool;
292- my $is_tag_zero = $product -> is_tag_zero_product;
248+ my $is_pool = $product -> lims-> is_pool; # Note - true for merged data.
293249
294- if ($self -> qc_to_run() eq ' spatial_filter' and ($self -> platform_NovaSeq or $self -> platform_NovaSeqX)) {
295- return 0;
250+ if ($self -> qc_to_run() eq ' spatial_filter'
251+ # Run on individual lanes only.
252+ return $is_lane && !($self -> platform_NovaSeq || $self -> platform_NovaSeqX) ? 1 : 0;
296253 }
297-
298- if ( $self -> _is_lane_level_check()) {
299- return ! $is_plex ;
254+ if ( $self -> qc_to_run() eq ' tag_metrics ' ) {
255+ # For indexed runs, run on individual lanes if they are pools of samples.
256+ return $self -> is_indexed() && $is_lane && $is_pool ? 1 : 0 ;
300257 }
301-
302- if ($self -> _is_lane_level_check4indexed_lane()) {
303- return $is_lane && $is_pool ;
258+ if ($self -> qc_to_run() eq ' review'
259+ # This check should never run on tag zero, other entities are fair game.
260+ if ($is_plex && $product -> is_tag_zero_product) {
261+ return 0;
262+ }
304263 }
305-
306- if ($self -> _is_check4target_file()) {
307- $can_run = (($is_lane && !$is_pool ) ||
308- ($is_plex && !$is_tag_zero ));
264+ if ($self -> qc_to_run() =~ $TARGET_FILE_CHECK_RE ) {
265+ # Do not run on tag zero files, unmerged or merged.
266+ # Do not run on lane-level data if the lane is a pool.
267+ # Run on lane-level data for a single library.
268+ # Run on merged plexes or lanes.
269+ if (($is_plex && $product -> is_tag_zero_product) || ($is_lane && $is_pool )) {
270+ return 0;
271+ }
309272 }
310273
311- if ( $ can_run) {
312- my %init_hash = ( rpt_list => $rpt_list , lims => $product -> lims );
313-
314- if ( $self -> has_repository && $self -> _check_uses_refrepos()) {
315- $init_hash { ' repository ' } = $self -> repository;
316- }
317- if ( $self -> qc_to_run() eq ' insert_size ' ) {
318- $init_hash { ' is_paired_read ' } = $ self-> is_paired_read () ? 1 : 0;
319- } elsif ( $self -> qc_to_run () eq ' review ' ) {
320- $init_hash { ' product_conf_file_path ' } = $self -> product_conf_file_path;
321- $init_hash {' runfolder_path ' $self -> runfolder_path ;
322- } elsif ( $self -> qc_to_run() eq ' genotype ' ) {
323- my $ref_fasta = npg_pipeline::cache::reference -> instance()
324- -> get_path( $product , q( fasta ) , $self -> repository());
325- if ( $ref_fasta ) {
326- $init_hash { ' reference_fasta ' } = $ ref_fasta;
327- }
274+ # The rest will abide by the return value of the can_run method of the
275+ # autoqc check. We have to provide enough argument to the constructor for
276+ # the object to be created and can_run to execute.
277+ my %init_hash = ( rpt_list => $product -> rpt_list, lims => $product -> lims );
278+ if ( $self -> has_repository && $self -> _check_uses_refrepos()) {
279+ $init_hash { ' repository ' } = $self -> repository;
280+ }
281+ if ( $ self-> qc_to_run () eq ' insert_size ' ) {
282+ $init_hash { ' is_paired_read ' } = $self -> is_paired_read () ? 1 : 0;
283+ } elsif ( $self -> qc_to_run() eq ' review ' ) {
284+ $init_hash {' product_conf_file_path ' $self -> product_conf_file_path ;
285+ $init_hash { ' runfolder_path ' } = $self -> runfolder_path;
286+ } elsif ( $self -> qc_to_run() eq ' genotype ' ) {
287+ my $ref_fasta = npg_pipeline::cache::reference -> instance()
288+ -> get_path( $product , q( fasta ) , $self -> repository());
289+ if ( $ ref_fasta) {
290+ $init_hash { ' reference_fasta ' } = $ref_fasta ;
328291 }
329-
330- my $class = $self -> _qc_module_name();
331- my $check_obj ;
332- try {
333- $check_obj = $class -> new(\%init_hash );
334- } catch {
335- delete $init_hash {' lims'
336- $check_obj = $class -> new(\%init_hash );
337- };
338-
339- $can_run = $check_obj -> can_run();
340292 }
341293
342- return $can_run ;
294+ my $class = $self -> _qc_module_name();
295+ my $check_obj ;
296+ try {
297+ $check_obj = $class -> new(\%init_hash );
298+ } catch {
299+ delete $init_hash {' lims'
300+ $check_obj = $class -> new(\%init_hash ); # Allow to fail at this stage.
301+ };
302+
303+ return $check_obj -> can_run();
343304}
344305
345306__PACKAGE__ -> meta-> make_immutable;
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