Merge pull request #681 from wtsi-npg/devel

merge from devel to master to create release 68.2.0

Changes

@@ -1,5 +1,15 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+release 68.2.0
+ - tweak for genome coverage figure in qc summary - fall back to target 
+   if no default autosomes only number available.
+ - a new script - npg_simple_robo4artic - to generate autoqc review
+   results from third party QC data
+ - skip ref_match autoqc checks only for true GBS samples
+ - SeqQC viewer: make visual cues for utility (user) QC  outcomes always
+   visible regardless of whether they concur with the manual QC outcome
+   or not
+
 release 68.1.0
  - criteria_md5 attribute is added to the review autoqc result object;
    previously it was computed at a point of loading to the database

MANIFEST

@@ -10,6 +10,7 @@ bin/mqc_outcome_reporter
 bin/npg_mqc_skipper
 bin/npg_qc_autoqc_data.pl
 bin/npg_qc_tag_sniff.pl
+bin/npg_simple_robo4artic
 bin/call_gtck_composite_rpt.pl
 bin/genotype_call_results_reporter
 Build.PL

bin/npg_simple_robo4artic

@@ -0,0 +1,208 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
+use Log::Log4perl qw(:levels);
+use Try::Tiny;
+use Carp;
+
+use npg_tracking::glossary::rpt;
+use npg_tracking::glossary::composition::factory::rpt_list;
+use npg_tracking::glossary::moniker;
+use npg_qc::autoqc::checks::review;
+
+our $VERSION = '0';
+
+Log::Log4perl->easy_init({layout => '%d %-5p %c - %m%n',
+                          level  => $INFO});
+my $logger = Log::Log4perl->get_logger();
+
+my $dir_out = $ARGV[0];
+if (defined $dir_out) {
+  if (($dir_out ne q[]) and (-d $dir_out) and (-w $dir_out)) {
+    $logger->info("Using output directory $dir_out");
+  } else {
+    $logger->error(
+      "Output directory $dir_out does not exists or is not writable");
+    exit 2;
+  }
+} else {
+  $logger->info('Using current directory as an output directory');
+}
+
+my $line_number = 0;
+##no critic (InputOutput::ProhibitExplicitStdin)
+while (my $line = <STDIN>) {
+##use critic
+  $line_number++;
+
+  if ($line =~ /\Asample_name,/smx) { # header, skip
+    next;
+  }
+  my $l = "Line $line_number:";
+  my $outcome;
+  my $file_name_root;
+  my $r;
+  my $sname;
+  my $lib_type;
+
+  try {
+    my @columns = split /,/xms, $line;
+    (@columns >= 2) or croak 'at least two columns are expected';
+    $file_name_root = shift @columns;
+    $file_name_root or croak 'no file name in the first column';
+    $outcome        = pop @columns;
+    defined $outcome or croak 'no outcome in the last column';
+    $outcome =~ s/\s+\Z//xms;
+    $outcome =~ /\A(TRUE|FALSE)\Z/xms or croak
+      "unexpected outcome value '$outcome'";
+
+    my $h = npg_tracking::glossary::moniker->parse_file_name($file_name_root);
+    my $rpt = npg_tracking::glossary::rpt->deflate_rpt($h);
+    $r = npg_qc::autoqc::checks::review->new(rpt_list => $rpt);
+    $sname = $r->lims->sample_supplier_name();
+    $lib_type = $r->lims->library_type();
+  } catch {
+    $logger->error("$l $_");
+    exit 1;
+  };
+
+  if (!$sname) {
+    $logger->warn(
+      "$l skipping $file_name_root, sample supplier name is not set");
+    next;
+  }
+
+  my ($name_prefix) = $sname =~ /\A([[:upper:]]{4})-/xms;
+  if (!$name_prefix || ($name_prefix =~ /\ACGAP\Z/ixms)) {
+    $logger->warn(
+      "$l skipping $file_name_root, sample '${sname}' does not belong to Heron");
+    next;
+  }
+
+  if (!$lib_type) {
+    $logger->warn(
+      "$l skipping $file_name_root, library type is not set");
+    next;
+  }
+
+  $r->result->pass(int($outcome eq 'TRUE' ? 1 : 0));
+  $r->result->qc_outcome($r->generate_qc_outcome('uqc', 'artic-qc'));
+  $r->result->library_type($lib_type);
+  my $condition = 'Passed ncov2019-artic-nf QC';
+  $r->result->evaluation_results({$condition => $r->result->pass});
+  $r->result->criteria({'and' => [$condition]});
+  try {
+    $r->result->store($dir_out);
+  } catch {
+    $logger->error("$l $_");
+    exit 2;
+  };
+}
+
+exit 0;
+
+__END__
+
+=head1 NAME
+
+npg_simple_robo4artic
+
+=head1 USAGE
+
+=head1 CONFIGURATION
+
+=head1 SYNOPSIS
+
+  echo '34014_1#104,TRUE'  | npg_simple_robo4artic
+  echo '34014_1#104,FALSE' | npg_simple_robo4artic 'my_dir'
+
+=head1 DESCRIPTION
+
+This script creates autoqc review result JSON files for
+entities and outcomes piped from STDIN. One line of input
+produces one file, unless this input is considered irrelevant.
+
+The JSON files are created in the working directory unless an
+alternative directory is specified as teh only argument. The
+qc outcomes are recorded as user QC.
+
+Example of input:
+
+34014_1#104,1.21,98.61,19221,34014_1#104.primertrimmed.consensus.fa,34014_1#104.mapped.primertrimmed.sorted.bam,TRUE
+34014_1#105,87.85,9.91,376,34014_1#105.primertrimmed.consensus.fa,34014_1#105.mapped.primertrimmed.sorted.bam,FALSE
+
+Only the first and the last column of the input is considered.
+
+=head1 REQUIRED ARGUMENTS
+
+None
+
+=head1 OPTIONS
+
+=head1 SUBROUTINES/METHODS
+
+=head1 DIAGNOSTICS
+
+=head1 CONFIGURATION AND ENVIRONMENT
+
+=head1 DEPENDENCIES
+
+=over
+
+=item strict
+
+=item warnings
+
+=item FindBin
+
+=item lib
+
+=item Carp
+
+=item Try::Tiny
+
+=item Log::Log4perl
+
+=item  npg_tracking::glossary::rpt
+
+=item npg_tracking::glossary::composition::factory::rpt_list
+
+=item npg_tracking::glossary::moniker
+
+=item npg_qc::autoqc::checks::review
+
+=back
+
+=head1 INCOMPATIBILITIES
+
+=head1 EXIT STATUS
+
+=head1 BUGS AND LIMITATIONS
+
+=head1 AUTHOR
+
+Marina Gourtovaia
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright (C) 2020 Genome Research Ltd.
+
+This file is part of NPG.
+
+NPG is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+=cut

lib/npg_qc/Schema/Mqc/OutcomeEntity.pm

@@ -173,7 +173,7 @@ sub sanitize_value {
   $value =~ s/\A\s+//smx;
   $value =~ s/\s+\Z//smx;
   $value or croak q[Only white space characters in input];
-  ($value =~ /\A[[:word:][:space:]#-]+\Z/smx) or croak 'Illegal characters';
+  ($value =~ /\A[[:word:][:space:]#-]+\Z/smx) or croak qq[Illegal characters in $value];
   return $value;
 }
 

lib/npg_qc/autoqc/checks/ref_match.pm

@@ -207,7 +207,8 @@ sub _scan_repository {
 override 'can_run' => sub {
   my $self = shift;
 
-  if($self->lims->gbs_plex_name){
+  if ($self->lims->gbs_plex_name &&
+     ($self->lims->library_type && $self->lims->library_type =~ /^GbS|GnT\sMDA/ismx)) {
     $self->result->add_comment('Ref match skipped for gbs plex libraries.');
     return 0;
   }

lib/npg_qc/autoqc/checks/review.pm

@@ -234,7 +234,8 @@ sub execute {
     $self->final_qc_outcome && croak $err;
     $self->result->add_comment($err);
   };
-  $self->result->qc_outcome($self->_generate_qc_outcome($md5));
+  $self->result->qc_outcome(
+    $self->generate_qc_outcome($self->_outcome_type(), $md5));
 
   return;
 }
@@ -270,6 +271,42 @@ sub evaluate {
   return $self->_apply_operator([values %{$emap}], $CONJUNCTION_OP);
 }
 
+=head2 generate_qc_outcome
+
+Returns a hash reference representing the QC outcome.
+
+  my $u_outcome = $r->generate_qc_outcome('uqc', $md5);
+  my $m_outcome = $r->generate_qc_outcome('mqc');
+
+=cut
+
+sub generate_qc_outcome {
+  my ($self, $outcome_type, $md5) = @_;
+
+  $outcome_type or croak 'outcome type should be defined';
+
+  my $package_name = 'npg_qc::Schema::Mqc::OutcomeDict';
+  my $pass = $self->result->pass;
+  #####
+  # Any of Accepted, Rejected, Undecided outcomes can be returned here
+  my $outcome = ($outcome_type eq $QC_TYPE_DEFAULT)
+    ? $package_name->generate_short_description(
+      $self->final_qc_outcome ? 1 : 0, $pass)
+    : $package_name->generate_short_description_prefix($pass);
+
+  $outcome_type .= '_outcome';
+  my $outcome_info = { $outcome_type => $outcome,
+                       timestamp   => create_current_timestamp(),
+                       username    => $ROBO_KEY};
+  if ($outcome_type =~ /\Auqc/xms) {
+    my @r = ($ROBO_KEY, $VERSION);
+    $md5 and push @r, $md5;
+    $outcome_info->{'rationale'} = join q[ ], @r;
+  }
+
+  return $outcome_info;
+}
+
 =head2 lims
 
 st::api::lims object corresponding ti this object's rpt_list
@@ -278,13 +315,12 @@ private attribute.
 
 =cut
 
-has '_lims' => (
+has 'lims' => (
   isa        => 'st::api::lims',
   is         => 'ro',
-  init_arg   => 'lims',
   lazy_build => 1,
 );
-sub _build__lims {
+sub _build_lims {
   my $self = shift;
   return st::api::lims->new(rpt_list => $self->rpt_list);
 }
@@ -299,7 +335,7 @@ sub _build__robo_config{
 
   my $message;
   my $strict = 1; # Parse study section only, ignore the default section.
-  my $config = $self->study_config($self->_lims(), $strict);
+  my $config = $self->study_config($self->lims(), $strict);
 
   if (keys %{$config}) {
     $config = $config->{$ROBO_KEY};
@@ -332,7 +368,7 @@ sub _build__criteria {
 
   (keys %{$self->_robo_config}) or return $rewritten;
 
-  my $lib_type = $self->_lims->library_type;
+  my $lib_type = $self->lims->library_type;
   $lib_type or croak 'Library type is not defined for ' .  $self->composition->freeze;
   # We are going to compare library type strings in lower case
   # because the case for this type of LIMs data might be inconsistent.
@@ -569,8 +605,8 @@ sub _evaluate_expression {
   return $evaluator->($obj);
 }
 
-sub _generate_qc_outcome {
-  my ($self, $md5) = @_;
+sub _outcome_type {
+  my $self = shift;
 
   my $outcome_type = $self->_robo_config()->{$QC_TYPE_KEY};
   if ($outcome_type) {
@@ -581,26 +617,7 @@ sub _generate_qc_outcome {
     $outcome_type = $QC_TYPE_DEFAULT;
   }
 
-  my $package_name = 'npg_qc::Schema::Mqc::OutcomeDict';
-  my $pass = $self->result->pass;
-  #####
-  # Any of Accepted, Rejected, Undecided outcomes can be returned here
-  my $outcome = ($outcome_type eq $QC_TYPE_DEFAULT)
-    ? $package_name->generate_short_description(
-      $self->final_qc_outcome ? 1 : 0, $pass)
-    : $package_name->generate_short_description_prefix($pass);
-
-  $outcome_type .= '_outcome';
-  my $outcome_info = { $outcome_type => $outcome,
-                       timestamp   => create_current_timestamp(),
-                       username    => $ROBO_KEY};
-  if ($outcome_type eq 'uqc') {
-    my @r = ($ROBO_KEY, $VERSION);
-    $md5 and push @r, $md5;
-    $outcome_info->{'rationale'} = join q[:], @r;
-  }
-
-  return $outcome_info;
+  return $outcome_type;
 }
 
 __PACKAGE__->meta->make_immutable();

npg_qc_viewer/root/src/about_qc_checks.tt2

@@ -255,7 +255,7 @@ target metrics separated by a pipe delimiter ;<br/><br/>
 <tr><th>Field</th><th>Description</th></tr>
 <tr><td>PP%</td><td>% mapped reads which are mapped in proper pairs - from Target region stats</td></tr>
 <tr><td>Gb</td><td>yield within target (bp) - from Target region stats</td></tr>
-<tr><td>Cov</td><td>% regions above coverage threshold - from Autosomes only target region stats</td></tr>
+<tr><td>Cov</td><td>% regions above coverage threshold - Autosomes only target region stats is the default value but if Autosomes only (denoted by small a) stats aren't available it will fall back to Target regions stats (denoted by a small t).</td></tr>
 </table>
 <br/><br/>
 <a name="verify bam id_check"></a>