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Merge devel to master for release 2.47.1 #445

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Feb 22, 2024
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6 changes: 0 additions & 6 deletions lib/WTSI/NPG/HTS/Illumina/RunPublisher.pm
Original file line number Diff line number Diff line change
Expand Up @@ -392,12 +392,6 @@ sub publish_index_files {
my ($name, $directory, $suffix) =
$self->parse_composition_filename($composition_file);

my $num_reads = $self->_find_num_reads($name);
if ($num_reads == 0) {
$self->debug("Skipping index files for $name: no reads");
return (0, 0, 0);
}

my $primary_avus = sub {
my ($obj) = @_;
return $self->make_primary_metadata
Expand Down
14 changes: 9 additions & 5 deletions t/lib/WTSI/NPG/HTS/Illumina/RunPublisherTest.pm
Original file line number Diff line number Diff line change
Expand Up @@ -481,7 +481,7 @@ sub publish_plex_pri_data_mlwh : Test(23) {
check_study_metadata($irods, $pkg, @absolute_paths);
}

sub publish_plex_sec_data_mlwh : Test(59) {
sub publish_plex_sec_data_mlwh : Test(64) {
note '=== Tests in publish_plex_sec_data_mlwh';
my $runfolder_path = "$data_path/sequence/150910_HS40_17550_A_C75BCANXX";
my $archive_path = "$runfolder_path/Data/Intensities/" .
Expand All @@ -500,9 +500,10 @@ sub publish_plex_sec_data_mlwh : Test(59) {
my $irods = WTSI::NPG::iRODS->new(environment => \%ENV,
strict_baton_version => 0);
my @observed = observed_data_objects($irods, $dest_coll, $dest_coll);
# No index files expected because the CRAM file contains no reads
# 17550_1#1.cram has no reads
my @expected = ("lane$lane/17550_1#1.bam_stats",
"lane$lane/17550_1#1.composition.json",
"lane$lane/17550_1#1.cram.crai",
"lane$lane/17550_1#1.flagstat",
"lane$lane/17550_1#1.markdups_metrics.txt",
"lane$lane/17550_1#1.seqchksum",
Expand Down Expand Up @@ -555,7 +556,7 @@ sub publish_plex_pri_data_samplesheet : Test(23) {
check_study_metadata($irods, $pkg, @absolute_paths);
}

sub publish_plex_sec_data_samplesheet : Test(59) {
sub publish_plex_sec_data_samplesheet : Test(64) {
note '=== Tests in publish_plex_sec_data_samplesheet';
my $runfolder_path = "$data_path/sequence/150910_HS40_17550_A_C75BCANXX";
my $archive_path = "$runfolder_path/Data/Intensities/" .
Expand All @@ -578,9 +579,10 @@ sub publish_plex_sec_data_samplesheet : Test(59) {
my $irods = WTSI::NPG::iRODS->new(environment => \%ENV,
strict_baton_version => 0);
my @observed = observed_data_objects($irods, $dest_coll, $dest_coll);
# No index files expected because the CRAM file contains no reads
# 17550_1#1.cram has no reads
my @expected = ("lane$lane/17550_1#1.bam_stats",
"lane$lane/17550_1#1.composition.json",
"lane$lane/17550_1#1.cram.crai",
"lane$lane/17550_1#1.flagstat",
"lane$lane/17550_1#1.markdups_metrics.txt",
"lane$lane/17550_1#1.seqchksum",
Expand Down Expand Up @@ -1008,7 +1010,9 @@ sub publish_archive_path_mlwh : Test(8) {

my ($num_files, $num_processed, $num_errors) = $pub->publish_files;

my $num_expected = 385;
# According to 18448_1.bam_flagstats.json, 18448_1.cram is empty
# The count below includes 18448_1.cram.crai
my $num_expected = 386;
cmp_ok($num_errors, '==', 0, 'No errors on publishing');
cmp_ok($num_processed, '==', $num_expected, "Published $num_expected files");

Expand Down
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