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Merge pull request #456 from ces/pacbio25
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Analysis loading changes post SMRT Link v13 - part 1
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@kjsanger
kjsanger authored Apr 22, 2024
2 parents ba9545d + 79137c3 commit c53aea0
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103 changes: 37 additions & 66 deletions MANIFEST
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Expand Up @@ -16298,6 +16298,7 @@ t/data/log_publisher/outgoing/100818_IL32_10371/RTALogs/20150909-1608_WarningLog
t/data/mlwh_json/illumina.json
t/data/mlwh_json/illumina_existing.json
t/data/mlwh_json/pacbio.json
t/data/mlwh_json/pacbio2.json
t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta
t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam
t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi
Expand Down Expand Up @@ -16615,17 +16616,6 @@ t/data/pacbio/sequel_analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0
t/data/pacbio/sequel_analysis/0000002152/outputs/barcode_ccs.report.json
t/data/pacbio/sequel_analysis/0000002152/outputs/ccs_processing.report.json
t/data/pacbio/sequel_analysis/0000002152/outputs/ccs.report.json
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.bam.pbi
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1009_BAK8A_OA--bc1009_BAK8A_OA.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000003280/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000003280/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml
t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam
t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi
t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml
Expand Down Expand Up @@ -16690,61 +16680,42 @@ t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/fl_transcripts.bc1012_5p--bc1012_3p.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000004117/cromwell-job/call-lima_isoseq/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000004117/entry-points/222a1be3-85b1-12b3-b3bc-9742f8e22f95.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.json
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.counts
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.report
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/lima_guesses_report.json
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi
t/data/pacbio/sequel_analysis/0000010313/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313_deplexfail/entry-points/cc8e3c72/m64229e_221104_164228.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.json
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.counts
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.guess.txt
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.report
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.lima.summary.txt
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.bam.pbi
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/demultiplex.unbarcoded.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/lima_guesses_report.json
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.bam.pbi
t/data/pacbio/sequel_analysis/0000010313_deplexfail/cromwell-job/call-lima/execution/bc1019_BAK8B_OA--bc1019_BAK8B_OA/demultiplex.bc1019_BAK8B_OA--bc1019_BAK8B_OA.consensusreadset.xml
t/data/pacbio/sequel_analysis/001185/entry-points/2c677e30-8918-4ef1-8649-f44adaac75d3.subreadset.xml
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.bam.pbi
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subreadset.xml
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.bam.pbi
t/data/pacbio/sequel_analysis/001185/tasks/barcoding.tasks.lima-0/lima.removed.subreadset.xml
t/data/pacbio/sequel_analysis/001612/entry-points/07d85801-6a09-4728-982c-e3c048f95bd8.subreadset.xml
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.bam
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.bam.pbi
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc12--lbc12.subreadset.xml
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.bam
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.bam.pbi
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lbc5--lbc5.subreadset.xml
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.counts
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.guess.txt
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.lima.summary.txt
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.bam
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.bam.pbi
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/lima_output.removed.subreadset.xml
t/data/pacbio/sequel_analysis/001612/tasks/barcoding.tasks.lima-0/merged_analysis_report.json
t/data/pacbio/sequel_analysis/000226/entry-points/acf46f00-12b8-45e6-bc10-b0790f8d6758.subreadset.xml
t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam
t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/m64016_190608_025655.ccs.bam.pbi
t/data/pacbio/sequel_analysis/000226/tasks/pbcoretools.tasks.auto_ccs_outputs-0/merged_analysis_report.json
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/lima_guesses.report.json
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi
t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/lima_guesses.report.json
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.json
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.counts
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.guess.txt
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.summary.txt
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.json
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi
t/data/pacbio/sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
t/data/pacbio/sequel_analysis/0000019480_deplexfail/outputs/m84098_240322_112047_s1.consensusreadset.xml
t/data/pacbio_meta_updater/m131209_183112_00127_c100579142550000001823092301191430_s1_p0.1.bax.h5
t/data/pacbio_seq_data_object/m54097_161031_165824.subreads.bam
t/data/pacbio_seq_data_object/m54097_161207_133626.subreads.bam
Expand Down
9 changes: 1 addition & 8 deletions bin/npg_pacbio_analysis_monitor.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,11 @@

Readonly::Scalar my $DEFAULT_INTERVAL_DAYS => 14;
Readonly::Scalar my $DEFAULT_OLDER_THAN_DAYS => 0;
Readonly::Scalar my $DEFAULT_SUBDIR => 0;

my $api_uri;
my $collection;
my $debug;
my $interval = $DEFAULT_INTERVAL_DAYS;
my $is_sub = $DEFAULT_SUBDIR;
my $log4perl_config;
my $older_than = $DEFAULT_OLDER_THAN_DAYS;
my $pipeline_name;
Expand All @@ -38,7 +36,6 @@
pod2usage(-verbose => 2, -exitval => 0);
},
'interval=i' => \$interval,
'is_sub' => \$is_sub,
'logconf=s' => \$log4perl_config,
'older-than|older_than=i' => \$older_than,
'pipeline-name|pipeline_name=s' => \$pipeline_name,
Expand All @@ -62,7 +59,6 @@

my @init_args = (interval => $interval,
irods => $irods,
is_sub => $is_sub,
mlwh_schema => $wh_schema,
older_than => $older_than,
);
Expand Down Expand Up @@ -110,7 +106,7 @@ =head1 NAME
=head1 SYNOPSIS
npg_pacbio_analysis_monitor
[--collection <path>] [--debug] [--interval days] [--is_sub]
[--collection <path>] [--debug] [--interval days]
[--logconf <path>] [--older-than days] [--pipeline_name <name>]
[--task_name <name>] [--api-uri] [--verbose]
Expand All @@ -120,9 +116,6 @@ =head1 SYNOPSIS
--debug Enable debug level logging. Optional, defaults to
false.
--help Display help.
--is_sub Data to be loaded is in sub-direcories of the
main analysis output directroy. Optional, defaults
to false.
--interval Interval of time in days for analysis loading.
Optional, defaults to 14.
Expand Down
14 changes: 2 additions & 12 deletions lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,14 @@ has 'pipeline_name' =>
(isa => 'Str',
is => 'ro',
required => 1,
default => 'pbsmrtpipe.pipelines.sa3_ds_barcode2',
default => 'cromwell.workflows.pb_demux_ccs',
documentation => 'A specified pipeline name to identify relevant jobs');

has 'task_name' =>
(isa => 'Str',
is => 'ro',
required => 1,
default => 'barcoding.tasks.lima-0',
default => 'call-lima/execution',
documentation => 'A specified task name to identify relevant output directories');

has 'job_root' =>
Expand All @@ -41,13 +41,6 @@ has 'job_root' =>
default => 'cromwell-job',
documentation => 'Root directory for job processing output');

has 'is_sub' =>
(isa => 'Bool',
is => 'ro',
required => 0,
default => 0,
documentation => 'Data to be loaded is in the sub-directories of main output directory');


=head2 publish_analysed_cells
Expand Down Expand Up @@ -119,9 +112,6 @@ sub _publish_analysis_path {
if ($self->dest_collection) {
push @init_args, dest_collection => $self->dest_collection;
}
if ($self->is_sub == 1 ) {
push @init_args, is_oninstrument => 1;
}

my $publisher = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new(@init_args);

Expand Down
25 changes: 18 additions & 7 deletions lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ our $SMT_METADATA_SET = q{hifi_reads.consensusreadset};

# Location of source metadata file
our $ENTRY_DIR = 'entry-points';
our $OUTPUT_DIR = 'outputs';

# Generic moviename file prefix
our $MOVIENAME_PATTERN = 'm[0-9a-z]+_\d+_\d+';
Expand All @@ -40,8 +41,8 @@ our $MOVIENAME_PATTERN = 'm[0-9a-z]+_\d+_\d+';
our $WELL_DIRECTORY_PATTERN = '\d+_[A-Z]\d+$';

# Additional sequence filenames permitted for loading
our @FNAME_PERMITTED = qw[fail_reads removed ccs hifi_reads fl_transcripts sequencing_control.subreads];
our @FNAME_NON_DEPLEXED = qw[unassigned removed sequencing_control.subreads];
our @FNAME_PERMITTED = qw[fail_reads removed ccs hifi_reads fl_transcripts sequencing_control.subreads unbarcoded];
our @FNAME_NON_DEPLEXED = qw[unassigned removed sequencing_control.subreads unbarcoded];
our @FNAME_FAILED = qw[fail_reads];

# Data processing level
Expand Down Expand Up @@ -323,7 +324,8 @@ sub list_files {
}
}
} else {
@files = $self->list_directory($self->runfolder_path, filter => $type);
@files = $self->list_directory
($self->runfolder_path, filter => $type, recurse => 1);
}

return \@files;
Expand Down Expand Up @@ -369,25 +371,34 @@ has '_metadata' =>
sub _build_metadata{
my ($self) = @_;

my $entry_path = catdir($self->analysis_path, $ENTRY_DIR);
my $entry_path = catdir($self->analysis_path, $ENTRY_DIR);
my $output_path = catdir($self->analysis_path, $OUTPUT_DIR);

my @metafiles;
if ($self->is_oninstrument == 1 && ! -d $entry_path && $self->is_smtwelve == 1) {
if (-d $output_path && ! -d $entry_path) {
# As all analysis cell based all metafiles should have the correct run name,
# well and plate number as no merged cell analysis - so just pick one.
my @files = $self->list_directory
($output_path, filter => $METADATA_SET .q[.]. $METADATA_FORMAT . q[$]);
push @metafiles, $files[0];
} elsif ($self->is_oninstrument == 1 && ! -d $entry_path && $self->is_smtwelve == 1) {
# Revio
@metafiles = $self->list_directory
($self->analysis_path,
filter => $self->movie_pattern .q[.]. $SMT_METADATA_SET .q[.]. $METADATA_FORMAT .q[$],
recurse => 1)
} elsif ($self->is_oninstrument == 1 && ! -d $entry_path) {
# Sequel IIe - as will never be upgraded from ICS v11
@metafiles = $self->list_directory
($self->analysis_path,
filter => $self->movie_pattern .q[.]. $METADATA_SET .q[.]. $METADATA_FORMAT .q[$])
} else {
} elsif (-d $entry_path) {
@metafiles = $self->list_directory
($entry_path, filter => $METADATA_FORMAT . q[$], recurse => 1);
}

if (@metafiles != 1) {
$self->logcroak('Expect one xml file in '. $self->analysis_path . ' (entry_dir)');
$self->logcroak('Expect one xml file in '. $self->analysis_path);
}
return WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
($metafiles[0], $METADATA_PREFIX);
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