diff --git a/Changes b/Changes
index 6cd8d4b06..ac64b7e91 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,12 @@
LIST OF CHANGES FOR NPG-QC PACKAGE
+release 67.1.0
+ - if DO_NOT_USE reference selected don't run VerifyBamID but provide
+ explanatory comment in json output file
+ - in qc store, capture error inferring a path to the archive dir,
+ which we need to retrieve autoqc data, rather from inferring
+ some other path
+
release 67.0.0
- fix regular expression used in collapser after change in template
- adapter check switched to use cram files; fixed an old bug in
diff --git a/lib/npg_qc/Schema/Result/VerifyBamId.pm b/lib/npg_qc/Schema/Result/VerifyBamId.pm
index d3d157af1..79cdef924 100644
--- a/lib/npg_qc/Schema/Result/VerifyBamId.pm
+++ b/lib/npg_qc/Schema/Result/VerifyBamId.pm
@@ -101,29 +101,25 @@ A foreign key referencing the id_seq_composition column of the seq_composition t
=head2 avg_depth
data_type: 'decimal'
- default_value: 0.00
- is_nullable: 0
+ is_nullable: 1
size: [11,2]
=head2 freemix
data_type: 'decimal'
- default_value: 0.00000
- is_nullable: 0
+ is_nullable: 1
size: [11,5]
=head2 freeLK0
data_type: 'decimal'
- default_value: 0.00
- is_nullable: 0
+ is_nullable: 1
size: [11,2]
=head2 freeLK1
data_type: 'decimal'
- default_value: 0.00
- is_nullable: 0
+ is_nullable: 1
size: [11,2]
=head2 pass
@@ -174,33 +170,13 @@ __PACKAGE__->add_columns(
'number_of_reads',
{ data_type => 'integer', is_nullable => 1 },
'avg_depth',
- {
- data_type => 'decimal',
- default_value => '0.00',
- is_nullable => 0,
- size => [11, 2],
- },
+ { data_type => 'decimal', is_nullable => 1, size => [11, 2] },
'freemix',
- {
- data_type => 'decimal',
- default_value => '0.00000',
- is_nullable => 0,
- size => [11, 5],
- },
+ { data_type => 'decimal', is_nullable => 1, size => [11, 5] },
'freeLK0',
- {
- data_type => 'decimal',
- default_value => '0.00',
- is_nullable => 0,
- size => [11, 2],
- },
+ { data_type => 'decimal', is_nullable => 1, size => [11, 2] },
'freeLK1',
- {
- data_type => 'decimal',
- default_value => '0.00',
- is_nullable => 0,
- size => [11, 2],
- },
+ { data_type => 'decimal', is_nullable => 1, size => [11, 2] },
'pass',
{ data_type => 'tinyint', is_nullable => 1 },
'comments',
@@ -274,8 +250,8 @@ __PACKAGE__->belongs_to(
with 'npg_qc::Schema::Composition', 'npg_qc::Schema::Flators', 'npg_qc::autoqc::role::result', 'npg_qc::autoqc::role::verify_bam_id';
-# Created by DBIx::Class::Schema::Loader v0.07047 @ 2017-09-14 16:25:18
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:fj9PpvtAIizcpJ0BvIj7hw
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2019-08-29 10:31:30
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:g2285gY2V+24Dah34YMHvQ
our $VERSION = '0';
diff --git a/lib/npg_qc/autoqc/checks/check.pm b/lib/npg_qc/autoqc/checks/check.pm
index ef0c86c3f..d2484903b 100644
--- a/lib/npg_qc/autoqc/checks/check.pm
+++ b/lib/npg_qc/autoqc/checks/check.pm
@@ -27,6 +27,7 @@ our $VERSION = '0';
Readonly::Scalar my $FILE_EXTENSION => 'fastq';
Readonly::Scalar my $HUMAN => q[Homo_sapiens];
+Readonly::Scalar my $DO_NOT_USE => q[DO_NOT_USE];
Readonly::Scalar my $FORWARD_READ_FILE_NAME_SUFFIX => q[1];
Readonly::Scalar my $REVERSE_READ_FILE_NAME_SUFFIX => q[2];
@@ -299,6 +300,26 @@ sub _build_result {
return $result;
}
+has '_lims_reference' => (isa => 'Maybe[Str]',
+ is => 'ro',
+ required => 0,
+ lazy_build => 1,
+ );
+
+sub _build__lims_reference {
+ my $self = shift;
+
+ if (!$self->can('lims')) {
+ $self->result->add_comment('lims accessor is not defined');
+ return;
+ }
+ if(!$self->lims->reference_genome) {
+ $self->result->add_comment('No reference genome specified');
+ return;
+ }
+ return $self->lims->reference_genome;
+}
+
=head2 run
Creates an object that can perform the requested test, calls test
@@ -467,29 +488,42 @@ sub create_filename {
=head2 entity_has_human_reference
Returns true if the reference_genome attribute is defined
-for the entiry and the value of the attribute indicates
+for the entity and the value of the attribute indicates
that the reference is for Homo Sapiens.
=cut
sub entity_has_human_reference {
my $self = shift;
-
- if (!$self->can('lims')) {
- $self->result->add_comment('lim saccessor is not defined');
- return 0;
- }
-
- my $ref = $self->lims->reference_genome;
- if(!$ref) {
- $self->result->add_comment('No reference genome specified');
+ if( !$self->_lims_reference ) {
return 0;
}
+ my $ref = $self->_lims_reference;
if($ref !~ /\A$HUMAN/smx) {
$self->result->add_comment("Non-human reference genome '$ref'");
return 0;
}
+ return 1;
+}
+=head2 entity_has_active_reference
+
+Returns true if the reference_genome attribute is defined for
+the entity and the value of the attribute indicates that the
+reference is not marked as do not use.
+
+=cut
+
+sub entity_has_active_reference {
+ my $self = shift;
+ if( !$self->_lims_reference ) {
+ return 0;
+ }
+ my $ref = $self->_lims_reference;
+ if($ref =~ /$DO_NOT_USE/smx) {
+ $self->result->add_comment("Non active reference genome used '$ref'");
+ return 0;
+ }
return 1;
}
diff --git a/lib/npg_qc/autoqc/checks/verify_bam_id.pm b/lib/npg_qc/autoqc/checks/verify_bam_id.pm
index 7f96d8c44..9fe9c49f6 100644
--- a/lib/npg_qc/autoqc/checks/verify_bam_id.pm
+++ b/lib/npg_qc/autoqc/checks/verify_bam_id.pm
@@ -81,6 +81,9 @@ override 'execute' => sub {
if(!$self->can_run()) {
return 1;
}
+ if (!$self->entity_has_active_reference()) {
+ return 1;
+ }
if (!$self->snv_file) {
croak q(Can't find snv file);
}
diff --git a/lib/npg_qc/autoqc/qc_store.pm b/lib/npg_qc/autoqc/qc_store.pm
index b27b216de..46675c68c 100644
--- a/lib/npg_qc/autoqc/qc_store.pm
+++ b/lib/npg_qc/autoqc/qc_store.pm
@@ -226,10 +226,24 @@ sub load_from_staging {
(ref $query eq $expected_type)
or croak qq[Query object should be of type $expected_type];
- my $rfo = $self->_runfolder_obj($query);
+ my $archive_path;
+ try {
+ $archive_path = npg_tracking::illumina::runfolder->new(
+ id_run => $query->id_run,
+ npg_tracking_schema => $query->npg_tracking_schema
+ )->archive_path;
+ } catch {
+ carp sprintf 'Failed to load data from staging for query "%s" : "%s"',
+ $query->to_string, $_;
+ };
- return $rfo ? $self->load_from_staging_archive($query, $rfo->archive_path)
- : npg_qc::autoqc::results::collection->new();
+ #####
+ # Potential error retrieving data from the archive directory is
+ # not captured; this is deliberate.
+ #
+ return $archive_path ?
+ $self->load_from_staging_archive($query, $archive_path) :
+ npg_qc::autoqc::results::collection->new();
}
=head2 load_from_staging_archive
@@ -518,25 +532,6 @@ sub _db_collection4compositions {
return npg_qc::autoqc::results::collection->new(results => \@rows);
}
-sub _runfolder_obj {
- my ($self, $query) = @_;
-
- my $rfs;
- try {
- $rfs = npg_tracking::illumina::runfolder->new(
- id_run => $query->id_run,
- npg_tracking_schema => $query->npg_tracking_schema
- );
- $rfs->analysis_path; # Might fail to find the run folder analysis directory.
- } catch {
- undef $rfs;
- carp sprintf 'Failed to load data from staging for query "%s" : "%s"',
- $query->to_string, $_;
- };
-
- return $rfs;
-}
-
sub _query_obj {
my ($self, $id_run, $lanes, $what, $db_lookup, $npg_schema) = @_;
diff --git a/npg_qc_viewer/root/src/ui_checks/verify_bam_id.tt2 b/npg_qc_viewer/root/src/ui_checks/verify_bam_id.tt2
index fd76ab5d0..6d4dbd9ef 100644
--- a/npg_qc_viewer/root/src/ui_checks/verify_bam_id.tt2
+++ b/npg_qc_viewer/root/src/ui_checks/verify_bam_id.tt2
@@ -3,6 +3,14 @@
[% has_reverse = check.reverse_read_gc_percent.defined -%]
+[% IF check.comments -%]
+
+
+| Comments | [% check.comments %] |
|---|
+
+
@@ -17,6 +25,4 @@
[%- END -%]
-
-
diff --git a/scripts/upgrade_schema/upgrade_schema-67.0.1 b/scripts/upgrade_schema/upgrade_schema-67.0.1
new file mode 100644
index 000000000..9be6c7a9f
--- /dev/null
+++ b/scripts/upgrade_schema/upgrade_schema-67.0.1
@@ -0,0 +1,10 @@
+--
+-- allow verify_bam_id decimal columns to be NULL
+--
+
+
+ALTER TABLE `verify_bam_id`
+MODIFY COLUMN `avg_depth` decimal(11,2) DEFAULT NULL,
+MODIFY COLUMN `freemix` decimal(11,5) DEFAULT NULL,
+MODIFY COLUMN `freeLK0` decimal(11,2) DEFAULT NULL,
+MODIFY COLUMN `freeLK1` decimal(11,2) DEFAULT NULL;
diff --git a/t/60-autoqc-checks-verify_bam_id.t b/t/60-autoqc-checks-verify_bam_id.t
index 7230542b4..60875dddd 100644
--- a/t/60-autoqc-checks-verify_bam_id.t
+++ b/t/60-autoqc-checks-verify_bam_id.t
@@ -2,7 +2,7 @@ use strict;
use warnings;
use Cwd;
use File::Temp qw(tempdir);
-use Test::More tests => 59;
+use Test::More tests => 64;
use Test::Exception;
use npg_tracking::util::abs_path qw(abs_path);
@@ -14,8 +14,9 @@ $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/autoqc];
my $tempdir = tempdir( CLEANUP => 1);
my $tool_path = "$tempdir/verifyBamID";
-my $bam_path = "$tempdir/13940_8.bam";
-for my $file (($tool_path, $bam_path)) {
+my $bam_path = "$tempdir/13940_8.bam";
+my $bam_path2 = "$tempdir/27483_8#6.bam";
+for my $file (($tool_path, $bam_path, $bam_path2)) {
open my $fh, '>', $file or die 'cannot open file for writing';
print $fh '#verifyBamID mock-up';
close $fh;
@@ -154,4 +155,21 @@ use_ok ('npg_qc::autoqc::checks::verify_bam_id');
ok($r->can_run, 'Can run on RNA library') or diag $r->result->comments;
}
+{
+ local $ENV{'NPG_CACHED_SAMPLESHEET_FILE'} = q[t/data/autoqc/verify_bam_id/samplesheet_27483.csv];
+ # Tests if
+ my $r = npg_qc::autoqc::checks::verify_bam_id->new(
+ rpt_list => '27483:8:6',
+ qc_in => $tempdir,
+ tmp_path => $tempdir,
+ repository => $repos,
+ snv_repository => $snv_repository_with_vcf);
+ lives_ok {$r->result;} 'No error creating result object';
+ ok(defined $r->ref_repository(), 'A default reference repository is set');
+ like($r->lims->reference_genome, qr/DO_NOT_USE/, 'human DO_NOT_USE reference genome');
+ ok($r->can_run, 'Can run on human DO_NOT_USE reference') or diag $r->result->comments;
+ $r->execute();
+ like($r->result->comments, qr/Non active reference genome/, 'Inappropriate ref comment recorded');
+}
+
1;
diff --git a/t/data/autoqc/verify_bam_id/samplesheet_27483.csv b/t/data/autoqc/verify_bam_id/samplesheet_27483.csv
index d1a4fec11..5e8fbfb1b 100644
--- a/t/data/autoqc/verify_bam_id/samplesheet_27483.csv
+++ b/t/data/autoqc/verify_bam_id/samplesheet_27483.csv
@@ -54,5 +54,5 @@ Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_t
8,22629979,CTTV0197621369,,GCTTTGGC,GGAAGACA,,RNA PolyA,GCTTTGGC,GGAAGACA,ncb@sanger.ac.uk slw@sanger.ac.uk,,ncb@sanger.ac.uk slw@sanger.ac.uk,,,0,0,23584446,0,22629979,,9606,S2263,,,standard,,,from:100 to:300,,,Homo sapiens,0,,CTTV0197621369,3840366,CTTV0197621369,,,188 IL22 8,888,EGAS00001001680,1,0,0,The purpose of this study is to establish whether intestinal organoid cultures from IBD patients are a good model of disease by studying various disease phenomena including%2C epithelial repair%2C wound healing%2C fibrotic changes%2C granulomas and inflammatory processes. Organoids will be used for target pertubation and validation studies. %0D%0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,4042,CTTV019 RNAseq,Homo_sapiens (GRCh38_15 %2B ensembl_78_transcriptome),0,Transcriptomes of intestinal organoids,3,
8,22629991,CTTV0197621370,,AACGACTG,GAAATTAT,,RNA PolyA,AACGACTG,GAAATTAT,ncb@sanger.ac.uk slw@sanger.ac.uk,,ncb@sanger.ac.uk slw@sanger.ac.uk,,,0,0,23584446,0,22629991,,9606,S2263,,,standard,,,from:100 to:300,,,Homo sapiens,0,,CTTV0197621370,3840367,CTTV0197621370,,,188 IL22 9,888,EGAS00001001680,1,0,0,The purpose of this study is to establish whether intestinal organoid cultures from IBD patients are a good model of disease by studying various disease phenomena including%2C epithelial repair%2C wound healing%2C fibrotic changes%2C granulomas and inflammatory processes. Organoids will be used for target pertubation and validation studies. %0D%0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,4042,CTTV019 RNAseq,Homo_sapiens (GRCh38_15 %2B ensembl_78_transcriptome),0,Transcriptomes of intestinal organoids,4,
8,22629908,CTTV0197621371,,GACCGTCA,CTTCTTGG,,RNA PolyA,GACCGTCA,CTTCTTGG,ncb@sanger.ac.uk slw@sanger.ac.uk,,ncb@sanger.ac.uk slw@sanger.ac.uk,,,0,0,23584446,0,22629908,,9606,S2263,,,standard,,,from:100 to:300,,,Homo sapiens,0,,CTTV0197621371,3840368,CTTV0197621371,,,Fut2 KO control 1,888,EGAS00001001680,1,0,0,The purpose of this study is to establish whether intestinal organoid cultures from IBD patients are a good model of disease by studying various disease phenomena including%2C epithelial repair%2C wound healing%2C fibrotic changes%2C granulomas and inflammatory processes. Organoids will be used for target pertubation and validation studies. %0D%0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,4042,CTTV019 RNAseq,Homo_sapiens (GRCh38_15 %2B ensembl_78_transcriptome),0,Transcriptomes of intestinal organoids,5,
-8,22629920,CTTV0197621372,,CTCTGGGT,ACTTCTCG,,RNA PolyA,CTCTGGGT,ACTTCTCG,ncb@sanger.ac.uk slw@sanger.ac.uk,,ncb@sanger.ac.uk slw@sanger.ac.uk,,,0,0,23584446,0,22629920,,9606,S2263,,,standard,,,from:100 to:300,,,Homo sapiens,0,,CTTV0197621372,3840369,CTTV0197621372,,,Fut2 KO control 2,888,EGAS00001001680,1,0,0,The purpose of this study is to establish whether intestinal organoid cultures from IBD patients are a good model of disease by studying various disease phenomena including%2C epithelial repair%2C wound healing%2C fibrotic changes%2C granulomas and inflammatory processes. Organoids will be used for target pertubation and validation studies. %0D%0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,4042,CTTV019 RNAseq,Homo_sapiens (GRCh38_15 %2B ensembl_78_transcriptome),0,Transcriptomes of intestinal organoids,6,
+8,22629920,CTTV0197621372,,CTCTGGGT,ACTTCTCG,,RNA PolyA,CTCTGGGT,ACTTCTCG,ncb@sanger.ac.uk slw@sanger.ac.uk,,ncb@sanger.ac.uk slw@sanger.ac.uk,,,0,0,23584446,0,22629920,,9606,S2263,,,standard,,,from:100 to:300,,,Homo sapiens,0,,CTTV0197621372,3840369,CTTV0197621372,,,Fut2 KO control 2,888,EGAS00001001680,1,0,0,The purpose of this study is to establish whether intestinal organoid cultures from IBD patients are a good model of disease by studying various disease phenomena including%2C epithelial repair%2C wound healing%2C fibrotic changes%2C granulomas and inflammatory processes. Organoids will be used for target pertubation and validation studies. %0D%0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,4042,CTTV019 RNAseq,Homo_sapiens (GRCh37_53) DO_NOT_USE,0,Transcriptomes of intestinal organoids,6,
8,22766063,phiX_for_spiked_buffers,,ACAACGCAATC,,,,ACAACGCAATC,,,,,,,1,0,23584446,0,22766063,,10847,,,,standard,,,,,,,0,,,1255141,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888,