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Allow non deplexed Revio cells to publish now #454

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Apr 8, 2024
Merged

Allow non deplexed Revio cells to publish now #454

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24 changes: 24 additions & 0 deletions MANIFEST
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Original file line number Diff line number Diff line change
Expand Up @@ -16577,6 +16577,30 @@ t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_11074
t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.summary.json
t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.csv.gz
t/data/pacbio/sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.json.gz
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.fail_reads.5mc_report.json
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.hifi_reads.5mc_report.json
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.pbreports.log
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz
t/data/pacbio/sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz
t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam
t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam.pbi
t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.consensusreadset.xml
Expand Down
27 changes: 17 additions & 10 deletions lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm
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Expand Up @@ -27,14 +27,11 @@ our $SEQUENCE_INDEX_FORMAT = 'pbi';
our $SEQUENCE_PRODUCT = 'subreads';
our $SEQUENCE_AUXILIARY = 'scraps';

# CCS Sequence file types - Sequel IIe
# CCS Sequence file types
our $CCS_SEQUENCE_PRODUCT = 'reads';
our $HIFI_SEQUENCE_PRODUCT = 'hifi_reads';
our $HIFIUB_SEQUENCE_PRODUCT = 'unbarcoded.hifi_reads';

# CCS Sequence file types - Revio
our $REV_HIFIUB_SEQ_PRODUCT = 'hifi_reads.unassigned';

our $REV_HIFIUB_SEQ_PRODUCT = 'hifi_reads.unassigned';

## Processing types
our $OFFINSTRUMENT = 'OffInstrument';
Expand All @@ -43,6 +40,7 @@ our $ONINSTRUMENTHO = 'OnInstrumentHifiOnly';
our $ONINSTRUMENTDP = 'OnInstrumentDeplex';
our $ONINSTRUMENTSR = 'OnInstrumentPlusSubreads';
our $ONINST_REVIO1 = 'OnInstrumentRevioOne';
our $ONINST_REVIO2 = 'OnInstrumentRevioTwo';

# Generic file prefix
our $FILE_PREFIX_PATTERN = 'm[0-9a-z]+_\d+_\d+';
Expand Down Expand Up @@ -97,6 +95,11 @@ sub _build_movie_pattern {
.q{[.]}. $REV_HIFIUB_SEQ_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT
.q{$}, undef, 1)->[0] ) {
$revio++;
} elsif ( defined $self->list_files($smrt_name, $REVIO_PREFIX_PATTERN
.q{[.]}. $HIFI_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT
.q{$}, undef, 1)->[0] ) {
## non deplexed data now supported for Revio
$revio++;
}
last if $revio > 0;
}
Expand Down Expand Up @@ -166,7 +169,8 @@ sub publish_files {
($num_files_cell, $num_processed_cell, $num_errors_cell) =
$self->_publish_on_instrument_cell($smrt_name, $process_type);
}
elsif ($process_type eq $ONINST_REVIO1) {
elsif (($process_type eq $ONINST_REVIO1) ||
($process_type eq $ONINST_REVIO2)) {
($num_files_cell, $num_processed_cell, $num_errors_cell) =
$self->_publish_revio_instrument_cell($smrt_name, $process_type);
}
Expand Down Expand Up @@ -211,7 +215,7 @@ sub _processing_type {
}
elsif (defined $self->list_files($smrt_name, $self->_movie_pattern .q{[.]}.
$HIFI_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT .q{$})->[0]) {
$type = $ONINSTRUMENTHO;
$type = ($self->_is_onrevio) ? $ONINST_REVIO2 : $ONINSTRUMENTHO;
}
elsif (defined $self->list_files($smrt_name, $self->_movie_pattern .q{[.]}.
$HIFIUB_SEQUENCE_PRODUCT .q{[.]}. $SEQUENCE_FILE_FORMAT .q{$})->[0]) {
Expand Down Expand Up @@ -325,8 +329,7 @@ sub _publish_revio_instrument_cell {

my $pub_xml = q[sts];

my ($nfb, $npb, $neb) = $self->_publish_deplexed_files
($smrt_name);
my ($nfb, $npb, $neb) = $self->_publish_deplexed_files($smrt_name);
my ($nfx, $npx, $nex) = $self->publish_xml_files
($smrt_name, $pub_xml);
my ($nfa, $npa, $nea) = $self->publish_aux_files
Expand Down Expand Up @@ -641,6 +644,9 @@ sub publish_image_archive {
q{hifi_reads.lima_summary.txt|summary.json|fail_reads.json|hifi_reads.json|}.
q{ccs_report.json|fail_reads.unassigned.json|hifi_reads.unassigned.json};
}
elsif ($process_type eq $ONINST_REVIO2) {
$file_types = q{ccs_report.txt|summary.json|ccs_report.json};
}

my $file_pattern1 = $self->_movie_pattern .q{.}. $file_types . q{$};
my $file_count = scalar split m/[|]/msx, $file_types;
Expand All @@ -649,7 +655,8 @@ sub publish_image_archive {
push @runfolder_files, @{$runfolder_file1};

# Optional 5mC report file
my $fmc_pattern = ($process_type eq $ONINST_REVIO1) ?
my $fmc_pattern =
(($process_type eq $ONINST_REVIO1) || ($process_type eq $ONINST_REVIO2)) ?
q{fail_reads.5mc_report.json|hifi_reads.5mc_report.json} : q{5mc_report.json};
my $file_pattern2 = $self->_movie_pattern .q{.}. $fmc_pattern .q{$};
my $runfolder_file2 = $self->list_files($smrt_name,$file_pattern2);
Expand Down
Empty file added ...bio/sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam
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Empty file added ...sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi
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Empty file added ...bio/sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam
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Empty file added ...sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi
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Empty file added t/data/pacbio/sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz
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Empty file added t/data/pacbio/sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt
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