From 9698868418081e5d1b924fa0cbead2fc01be729d Mon Sep 17 00:00:00 2001
From: Carol Scott <ces@sanger.ac.uk>
Date: Tue, 17 Sep 2024 17:37:36 +0100
Subject: [PATCH 1/3] Remove sequel specific references from the code

---
 MANIFEST                                      | 1009 ++++++++---------
 .../PacBio/{Sequel => }/AnalysisMonitor.pm    |   13 +-
 .../PacBio/{Sequel => }/AnalysisPublisher.pm  |   16 +-
 .../NPG/HTS/PacBio/AnalysisPublisherBase.pm   |    4 +-
 .../HTS/PacBio/{Sequel => }/AnalysisReport.pm |    8 +-
 .../HTS/PacBio/{Sequel => }/ImageArchive.pm   |    4 +-
 .../PacBio/{Sequel => }/IsoSeqPublisher.pm    |   10 +-
 .../HTS/PacBio/{Sequel => }/MetaXMLParser.pm  |    4 +-
 lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm        |   30 +
 .../NPG/HTS/PacBio/{Sequel => }/Product.pm    |    4 +-
 .../NPG/HTS/PacBio/{Sequel => }/Reportdata.pm |    4 +-
 .../NPG/HTS/PacBio/{Sequel => }/RunAuditor.pm |    7 +-
 .../NPG/HTS/PacBio/{Sequel => }/RunDelete.pm  |    4 +-
 .../PacBio/{Sequel => }/RunDeleteMonitor.pm   |   11 +-
 .../NPG/HTS/PacBio/{Sequel => }/RunMonitor.pm |    7 +-
 .../HTS/PacBio/{Sequel => }/RunPublisher.pm   |   26 +-
 .../PacBio/{Sequel => }/RunPublisherBase.pm   |   10 +-
 lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm |   69 --
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 .../execution/merged_analysis_report.json     |    1 +
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 .../{Sequel => }/AnalysisMonitorTest.pm       |    8 +-
 .../{Sequel => }/AnalysisPublisherTest.pm     |   22 +-
 .../PacBio/{Sequel => }/AnalysisReportTest.pm |   30 +-
 .../PacBio/{Sequel => }/ImageArchiveTest.pm   |   34 +-
 .../{Sequel => }/IsoSeqPublisherTest.pm       |   14 +-
 .../HTS/PacBio/{Sequel => }/RunAuditorTest.pm |   16 +-
 .../{Sequel => }/RunDeleteMonitorTest.pm      |   28 +-
 .../HTS/PacBio/{Sequel => }/RunDeleteTest.pm  |   12 +-
 .../HTS/PacBio/{Sequel => }/RunMonitorTest.pm |   10 +-
 .../PacBio/{Sequel => }/RunPublisherTest.pm   |   66 +-
 t/pacbio_analysis_monitor.t                   |    7 +
 t/pacbio_analysis_publisher.t                 |    7 +
 t/pacbio_analysis_report.t                    |    7 +
 t/pacbio_image_archive.t                      |    7 +
 t/pacbio_isoseq_publisher.t                   |    7 +
 t/pacbio_run_auditor.t                        |    6 +
 t/pacbio_run_delete.t                         |    6 +
 t/pacbio_run_delete_monitor.t                 |    6 +
 t/pacbio_run_monitor.t                        |    7 +
 t/pacbio_run_publisher.t                      |    7 +
 t/pacbio_sequel_analysis_monitor.t            |    7 -
 t/pacbio_sequel_analysis_publisher.t          |    7 -
 t/pacbio_sequel_analysis_report.t             |    7 -
 t/pacbio_sequel_image_archive.t               |    7 -
 t/pacbio_sequel_isoseq_publisher.t            |    7 -
 t/pacbio_sequel_run_auditor.t                 |    6 -
 t/pacbio_sequel_run_delete.t                  |    6 -
 t/pacbio_sequel_run_delete_monitor.t          |    6 -
 t/pacbio_sequel_run_monitor.t                 |    7 -
 t/pacbio_sequel_run_publisher.t               |    7 -
 528 files changed, 789 insertions(+), 833 deletions(-)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisMonitor.pm (92%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisPublisher.pm (96%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisReport.pm (95%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/ImageArchive.pm (98%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/IsoSeqPublisher.pm (97%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/MetaXMLParser.pm (98%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/Product.pm (96%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/Reportdata.pm (95%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunAuditor.pm (96%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunDelete.pm (95%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunDeleteMonitor.pm (90%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunMonitor.pm (93%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunPublisher.pm (97%)
 rename lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunPublisherBase.pm (94%)
 delete mode 100644 lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam} (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.consensusreadset.xml} (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.counts (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.guess.txt (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.summary.txt (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam} (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam => analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.consensusreadset.xml} (100%)
 create mode 100644 t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/outputs/barcode_ccs.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/outputs/ccs.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000002152/outputs/ccs_processing.report.json (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam} (100%)
 rename t/data/pacbio/{sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.transferdone => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml} (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt (100%)
 rename t/data/pacbio/{sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam.pbi => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam} (100%)
 rename t/data/pacbio/{sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.baz2bam_1.log => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs.log => analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml} (100%)
 create mode 100644 t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot.png (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot_thumb.png (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/readlength_plot.png (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/readlength_plot_thumb.png (100%)
 rename t/data/pacbio/{sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima.log => analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam} (100%)
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 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.zmw_metrics.csv.gz => analysis/0000020083/outputs/segmented.non_passing.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.zmw_metrics.json.gz => analysis/0000020083/outputs/transcripts-1.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.default.bam => analysis/0000020083/outputs/transcripts-2.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.default.bam.pbi => analysis/0000020083/outputs/transcripts-3.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.unassigned.bam => analysis/0000020083/outputs/transcripts-4.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.unassigned.bam.pbi => analysis/0000020083/outputs/transcripts-5.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.default.bam => analysis/0000020156/outputs/collapse_isoforms.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.default.bam.pbi => analysis/0000020156/outputs/collapse_isoforms.fl_count.txt} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.unassigned.bam => analysis/0000020156/outputs/collapse_isoforms.flnc_count.txt} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.unassigned.bam.pbi => analysis/0000020156/outputs/collapse_isoforms.gff} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/m84047_230404_172053_s2.primary_qc.tar.xz => analysis/0000020156/outputs/collapse_isoforms.group.txt} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.basecaller.log => analysis/0000020156/outputs/collapse_isoforms.read_stat.txt} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.baz2bam.log => analysis/0000020156/outputs/flnc-1.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.canary => analysis/0000020156/outputs/flnc-2.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.fail_reads.lima.log => analysis/0000020156/outputs/flnc-3.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.fail_reads.primrose.log => analysis/0000020156/outputs/flnc-4.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.hifi_reads.lima.log => analysis/0000020156/outputs/flnc-5.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.hifi_reads.primrose.log => analysis/0000020156/outputs/flnc.report-1.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/metadata/nvidia-smi.log => analysis/0000020156/outputs/flnc.report-2.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.lima_report.txt => analysis/0000020156/outputs/flnc.report-3.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.lima_report.txt => analysis/0000020156/outputs/flnc.report-4.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.reports.zip => analysis/0000020156/outputs/flnc.report-5.csv} (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000020156/outputs/isoseq.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000020156/outputs/isoseq_mapping.report.json (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000020156/outputs/isoseq_primers.report.json (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.zmw_metrics.csv.gz => analysis/0000020156/outputs/mapped.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.zmw_metrics.json.gz => analysis/0000020156/outputs/mapped.bam.bai} (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000020156/outputs/read_segmentation.report.json (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.bc1010_BAK8A_OA.bam => analysis/0000020156/outputs/sample0.transcripts.cluster_report.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.bc1010_BAK8A_OA.bam.pbi => analysis/0000020156/outputs/sample0.transcripts.fl_counts.csv} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.unassigned.bam => analysis/0000020156/outputs/segmented.bam} (100%)
 rename t/data/pacbio/{sequel_analysis => analysis}/0000020156/outputs/segmented.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.unassigned.bam.pbi => analysis/0000020156/outputs/segmented.non_passing.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam => analysis/0000020156/outputs/transcripts.fasta} (100%)
 delete mode 100644 t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
 delete mode 100644 t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
 delete mode 100644 t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/merged_analysis_report.json
 delete mode 100644 t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam.pbi => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam.pbi => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/m84047_230404_175159_s3.primary_qc.tar.xz => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.basecaller.log => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.baz2bam.log => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.lima.log => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel => sequence}/r54097_20170727_165601/1_A02/m54097_170727_170646.subreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.primrose.log => sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.transferdone} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.bc1015_BAK8B_OA--bc1015_BAK8B_OA.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.hifi_reads.lima.log => sequence/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.hifi_reads.primrose.log => sequence/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam.pbi} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.barcodes.fasta (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/metadata/nvidia-smi.log => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.baz2bam_1.log} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.lima_report.txt => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs_reports.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs_reports.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.lima_report.txt => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_guess.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_guess.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.reports.zip => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.zmw_metrics.csv.gz => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.primrose.log} (100%)
 rename t/data/pacbio/{sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.zmw_metrics.json.gz => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.sts.xml} (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.bc2076.bam => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.transferdone} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.bc2076.bam.pbi => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.hifi_reads.bam} (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.unassigned.bam => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.hifi_reads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.unassigned.bam.pbi => sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.bc1011_BAK8A_OA--bc1011_BAK8A_OA.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.bc2076.bam => sequence/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.bc2076.bam.pbi => sequence/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam.pbi} (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/1_A01/m64089e_220930_165238.5mc_report.json (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.unassigned.bam => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.ccs_reports.txt} (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/1_A01/m64089e_220930_165238.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.unassigned.bam.pbi => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_counts.txt} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/m84098_240219_110741_s1.primary_qc.tar.xz => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_guess.json} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.basecaller.log => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_guess.txt} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.baz2bam.log => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_report.txt} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.ccs.log => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_summary.txt} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sequencing_control.subreads.bam => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.primary_qc.tar.xz} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sequencing_control.subreads.bam.pbi => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.sts.xml} (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sts.xml => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.hifi_reads.bam} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.lima_report.txt => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.hifi_reads.bam.pbi} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.lima_report.txt => sequence/r64089e_20220930_164018/1_A01/m64089e_220930_165238.zmw_metrics.json.gz} (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/1_A01/merged_analysis_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.bc1012_BAK8A_OA--bc1012_BAK8A_OA.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.pbreports.log => sequence/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.hifi_reads.bc1012_BAK8A_OA--bc1012_BAK8A_OA.bam} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.reports.zip => sequence/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.hifi_reads.bc1012_BAK8A_OA--bc1012_BAK8A_OA.bam.pbi} (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/2_B01/m64089e_221001_201630.5mc_report.json (100%)
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 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/2_B01/m64089e_221001_201630.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.csv.gz => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_counts.txt} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.json.gz => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_guess.json} (100%)
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 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_guess.txt} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_report.txt} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_summary.txt} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.primary_qc.tar.xz} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.sts.xml} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.hifi_reads.bam} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.hifi_reads.bam.pbi} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi => sequence/r64089e_20220930_164018/2_B01/m64089e_221001_201630.zmw_metrics.json.gz} (100%)
 mode change 100644 => 100755
 rename t/data/pacbio/{sequel => sequence}/r64089e_20220930_164018/2_B01/merged_analysis_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r64094e_20221214_160714/1_A01/m64094e_221214_161800.ccs_reports.json (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.ccs_reports.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64094e_20221214_160714/1_A01/m64094e_221214_161800.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.pbreports.log => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.reads.bam} (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.reads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.sts.xml} (100%)
 rename t/data/pacbio/{sequel/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.subreads.bam} (100%)
 rename 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 => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.subreads.bam.pbi} (100%)
 rename 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 => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.transferdone} (100%)
 rename 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 => sequence/r64094e_20221214_160714/1_A01/m64094e_221214_161800.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64174e_20210114_161659/1_A01/m64174e_210114_162751.ccs_reports.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.ccs_reports.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r64174e_20210114_161659/1_A01/m64174e_210114_162751.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam.pbi => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.consensusreadset.xml => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.reads.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.reads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.sts.xml} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.transferdone} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam => sequence/r64174e_20210114_161659/1_A01/m64174e_210114_162751.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi => sequence/r84047_20230404_164149/1_A01/fail_reads/m84047_230404_164952_s1.fail_reads.bc2073.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml => sequence/r84047_20230404_164149/1_A01/fail_reads/m84047_230404_164952_s1.fail_reads.bc2073.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam => sequence/r84047_20230404_164149/1_A01/fail_reads/m84047_230404_164952_s1.fail_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam.bai => sequence/r84047_20230404_164149/1_A01/fail_reads/m84047_230404_164952_s1.fail_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/m64089e_210503_164858.hifi_reads.bam.pbi => sequence/r84047_20230404_164149/1_A01/hifi_reads/m84047_230404_164952_s1.hifi_reads.bc2073.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam => sequence/r84047_20230404_164149/1_A01/hifi_reads/m84047_230404_164952_s1.hifi_reads.bc2073.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi => sequence/r84047_20230404_164149/1_A01/hifi_reads/m84047_230404_164952_s1.hifi_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report => sequence/r84047_20230404_164149/1_A01/hifi_reads/m84047_230404_164952_s1.hifi_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam => sequence/r84047_20230404_164149/1_A01/m84047_230404_164952_s1.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.barcodes.fasta (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.basecaller.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.baz2bam.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.canary (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.ccs.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.lima.report => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.darkcal.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.fail_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/m84098_240322_112047_s1.unbarcoded.bam.pbi => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.fail_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-1.fasta => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.hifi_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-1.gff => sequence/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.hifi_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.nrt_find.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.sts.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/metadata/m84047_230404_164952_s1.transferdone (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.fail_reads.bc2073.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.fail_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.fail_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.fail_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.hifi_reads.bc2073.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.hifi_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.hifi_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/pb_formats/m84047_230404_164952_s1.hifi_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.ccs_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.ccs_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.fail_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.fail_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-2.fasta => sequence/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.fail_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.fail_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.fail_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.hifi_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.hifi_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-2.gff => sequence/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.hifi_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.hifi_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.hifi_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-3.fasta => sequence/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.reports.zip} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.summary.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-3.gff => sequence/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.zmw_metrics.csv.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-4.fasta => sequence/r84047_20230404_164149/1_A01/statistics/m84047_230404_164952_s1.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-4.gff => sequence/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.default.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-5.fasta => sequence/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.default.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms-5.gff => sequence/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-1.txt => sequence/r84047_20230404_164149/1_B01/fail_reads/m84047_230404_172053_s2.fail_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-2.txt => sequence/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.default.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-3.txt => sequence/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.default.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-4.txt => sequence/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.flnc_count-5.txt => sequence/r84047_20230404_164149/1_B01/hifi_reads/m84047_230404_172053_s2.hifi_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.group-1.txt => sequence/r84047_20230404_164149/1_B01/m84047_230404_172053_s2.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.barcodes.fasta (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.group-2.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.basecaller.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.group-3.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.baz2bam.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.group-4.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.canary} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.ccs.log (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.darkcal.log (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.group-5.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.fail_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-1.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.fail_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-2.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.hifi_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-3.txt => sequence/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.hifi_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.nrt_find.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.sts.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/metadata/m84047_230404_172053_s2.transferdone (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-4.txt => sequence/r84047_20230404_164149/1_B01/metadata/nvidia-smi.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.fail_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.fail_reads.default.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.fail_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.fail_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.hifi_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.hifi_reads.default.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.hifi_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/pb_formats/m84047_230404_172053_s2.hifi_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.ccs_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.ccs_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/collapse_isoforms.read_stat-5.txt => sequence/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.fail_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc-1.bam => sequence/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.hifi_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc-2.bam => sequence/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.reports.zip} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.summary.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc-3.bam => sequence/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.zmw_metrics.csv.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc-4.bam => sequence/r84047_20230404_164149/1_B01/statistics/m84047_230404_172053_s2.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc-5.bam => sequence/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.bc1010_BAK8A_OA.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc.report-1.csv => sequence/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.bc1010_BAK8A_OA.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc.report-2.csv => sequence/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc.report-3.csv => sequence/r84047_20230404_164149/1_C01/fail_reads/m84047_230404_175159_s3.fail_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc.report-4.csv => sequence/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/flnc.report-5.csv => sequence/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped-1.bam => sequence/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped-2.bam => sequence/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped-3.bam => sequence/r84047_20230404_164149/1_C01/m84047_230404_175159_s3.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.barcodes.fasta (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped-4.bam => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.basecaller.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped-5.bam => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.baz2bam.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.canary (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.ccs.log (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.darkcal.log (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped.bam-1.bai => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped.bam-2.bai => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped.bam-3.bai => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.hifi_reads.lima.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped.bam-4.bai => sequence/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.hifi_reads.primrose.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.nrt_find.txt (100%)
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 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.transferdone (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/mapped.bam-5.bai => sequence/r84047_20230404_164149/1_C01/metadata/nvidia-smi.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.fail_reads.bc1010_BAK8A_OA.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.fail_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.fail_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.fail_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.hifi_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.hifi_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/pb_formats/m84047_230404_175159_s3.hifi_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.ccs_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.ccs_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample0.transcripts.cluster_report.csv => sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample0.transcripts.fl_counts.csv => sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.hifi_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample1.transcripts.cluster_report.csv => sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.reports.zip} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.summary.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample1.transcripts.fl_counts.csv => sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.zmw_metrics.csv.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample2.transcripts.cluster_report.csv => sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample2.transcripts.fl_counts.csv => sequence/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.bc2076.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample3.transcripts.cluster_report.csv => sequence/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.bc2076.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample3.transcripts.fl_counts.csv => sequence/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample4.transcripts.cluster_report.csv => sequence/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/sample4.transcripts.fl_counts.csv => sequence/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.bc2076.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/segmented.bam => sequence/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.bc2076.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/segmented.non_passing.bam => sequence/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.unassigned.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/transcripts-1.fasta => sequence/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.unassigned.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/transcripts-2.fasta => sequence/r84098_20240219_101849/1_A01/m84098_240219_110741_s1.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.barcodes.fasta (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/transcripts-3.fasta => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.basecaller.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/transcripts-4.fasta => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.baz2bam.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020083/outputs/transcripts-5.fasta => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.ccs.log} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.metadata.xml (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.fasta => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sequencing_control.subreads.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.fl_count.txt => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sequencing_control.subreads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.flnc_count.txt => sequence/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.sts.xml} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1.transferdone (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1_basic_preview_4hr.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/metadata/m84098_240219_110741_s1_full_preview_23hr.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.fail_reads.bc2076.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.fail_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.fail_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.fail_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.hifi_reads.bc2076.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.hifi_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.hifi_reads.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/pb_formats/m84098_240219_110741_s1.hifi_reads.unassigned.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.ccs_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.ccs_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.gff => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.fail_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.lima_counts.txt (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.group.txt => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.lima_report.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.lima_summary.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.hifi_reads.unassigned.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/collapse_isoforms.read_stat.txt => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.pbreports.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc-1.bam => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.reports.zip} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.summary.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc-2.bam => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.csv.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc-3.bam => sequence/r84098_20240219_101849/1_A01/statistics/m84098_240219_110741_s1.zmw_metrics.json.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc-4.bam => sequence/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc-5.bam => sequence/r84098_20240321_105751/1_A01/fail_reads/m84098_240321_114027_s1.fail_reads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc.report-1.csv => sequence/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc.report-2.csv => sequence/r84098_20240321_105751/1_A01/hifi_reads/m84098_240321_114027_s1.hifi_reads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc.report-3.csv => sequence/r84098_20240321_105751/1_A01/m84098_240321_114027_s1.primary_qc.tar.xz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc.report-4.csv => sequence/r84098_20240321_105751/1_A01/metadata/Transfer_Test_240321_105751.txt} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.metadata.xml (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/flnc.report-5.csv => sequence/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/mapped.bam => sequence/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sequencing_control.subreads.bam.pbi} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/mapped.bam.bai => sequence/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.sts.xml} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/sample0.transcripts.cluster_report.csv => sequence/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1.transferdone} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_basic_preview_4hr.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/metadata/m84098_240321_114027_s1_full_preview_23hr.metadata.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.fail_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/pb_formats/m84098_240321_114027_s1.hifi_reads.consensusreadset.xml (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.ccs_report.txt (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.fail_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.hifi_reads.5mc_report.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/sample0.transcripts.fl_counts.csv => sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.pbreports.log} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/segmented.bam => sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.reports.zip} (100%)
 rename t/data/pacbio/{sequel => sequence}/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.summary.json (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/segmented.non_passing.bam => sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.csv.gz} (100%)
 rename t/data/pacbio/{sequel_analysis/0000020156/outputs/transcripts.fasta => sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz} (100%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisMonitorTest.pm (93%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisPublisherTest.pm (95%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/AnalysisReportTest.pm (72%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/ImageArchiveTest.pm (79%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/IsoSeqPublisherTest.pm (96%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunAuditorTest.pm (93%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunDeleteMonitorTest.pm (93%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunDeleteTest.pm (68%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunMonitorTest.pm (94%)
 rename t/lib/WTSI/NPG/HTS/PacBio/{Sequel => }/RunPublisherTest.pm (94%)
 create mode 100644 t/pacbio_analysis_monitor.t
 create mode 100644 t/pacbio_analysis_publisher.t
 create mode 100644 t/pacbio_analysis_report.t
 create mode 100644 t/pacbio_image_archive.t
 create mode 100644 t/pacbio_isoseq_publisher.t
 create mode 100644 t/pacbio_run_auditor.t
 create mode 100644 t/pacbio_run_delete.t
 create mode 100644 t/pacbio_run_delete_monitor.t
 create mode 100644 t/pacbio_run_monitor.t
 create mode 100644 t/pacbio_run_publisher.t
 delete mode 100644 t/pacbio_sequel_analysis_monitor.t
 delete mode 100644 t/pacbio_sequel_analysis_publisher.t
 delete mode 100644 t/pacbio_sequel_analysis_report.t
 delete mode 100644 t/pacbio_sequel_image_archive.t
 delete mode 100644 t/pacbio_sequel_isoseq_publisher.t
 delete mode 100644 t/pacbio_sequel_run_auditor.t
 delete mode 100644 t/pacbio_sequel_run_delete.t
 delete mode 100644 t/pacbio_sequel_run_delete_monitor.t
 delete mode 100644 t/pacbio_sequel_run_monitor.t
 delete mode 100644 t/pacbio_sequel_run_publisher.t

diff --git a/MANIFEST b/MANIFEST
index 77ccf06e..c1447e0c 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -57,30 +57,29 @@ lib/WTSI/NPG/HTS/Illumina/RunPublisher.pm
 lib/WTSI/NPG/HTS/Illumina/XMLDataObject.pm
 lib/WTSI/NPG/HTS/LIMSFactory.pm
 lib/WTSI/NPG/HTS/Metadata.pm
+lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm
 lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
+lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm
+lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm
 lib/WTSI/NPG/HTS/PacBio/Annotator.pm
 lib/WTSI/NPG/HTS/PacBio/DataObjectFactory.pm
+lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm
+lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm
 lib/WTSI/NPG/HTS/PacBio/Metadata.pm
 lib/WTSI/NPG/HTS/PacBio/MetaQuery.pm
 lib/WTSI/NPG/HTS/PacBio/MetaUpdater.pm
+lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm
 lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
+lib/WTSI/NPG/HTS/PacBio/Product.pm
 lib/WTSI/NPG/HTS/PacBio/PublisherBase.pm
+lib/WTSI/NPG/HTS/PacBio/Reportdata.pm 
+lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm
+lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitor.pm
+lib/WTSI/NPG/HTS/PacBio/RunDelete.pm
+lib/WTSI/NPG/HTS/PacBio/RunMonitor.pm
+lib/WTSI/NPG/HTS/PacBio/RunPublisherBase.pm
+lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm
 lib/WTSI/NPG/HTS/PacBio/SeqDataObject.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReport.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitor.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitor.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherBase.pm
-lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm
 lib/WTSI/NPG/HTS/PathLister.pm
 lib/WTSI/NPG/HTS/PublishState.pm
 lib/WTSI/NPG/HTS/RunPublisher.pm
@@ -16301,476 +16300,476 @@ 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
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreadset.xml
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz
-t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.transferdone
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.5mc_report.json
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.barcodes.fasta
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.baz2bam_1.log
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs.log
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs_reports.json
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs_reports.txt
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_counts.txt
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_guess.json
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_guess.txt
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima.log
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_report.txt
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.lima_summary.txt
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.primary_qc.tar.xz
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.primrose.log
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.sts.xml
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.transferdone
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.hifi_reads.bam
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.unbarcoded.hifi_reads.bam.pbi
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.zmw_metrics.json.gz
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.bc1015_BAK8B_OA--bc1015_BAK8B_OA.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam
-t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam.pbi
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.5mc_report.json
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.ccs_reports.json
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.ccs_reports.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_counts.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_guess.json
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_guess.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_report.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.lima_summary.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.primary_qc.tar.xz
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.sts.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.hifi_reads.bam
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.unbarcoded.hifi_reads.bam.pbi
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/m64089e_220930_165238.zmw_metrics.json.gz
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/merged_analysis_report.json
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.bc1011_BAK8A_OA--bc1011_BAK8A_OA.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam
-t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam.pbi
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.5mc_report.json
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.ccs_reports.json
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.ccs_reports.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_counts.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_guess.json
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_guess.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_report.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.lima_summary.txt
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.primary_qc.tar.xz
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.sts.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.hifi_reads.bam
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.unbarcoded.hifi_reads.bam.pbi
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/m64089e_221001_201630.zmw_metrics.json.gz
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/merged_analysis_report.json
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.bc1012_BAK8A_OA--bc1012_BAK8A_OA.consensusreadset.xml
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.hifi_reads.bc1012_BAK8A_OA--bc1012_BAK8A_OA.bam
-t/data/pacbio/sequel/r64089e_20220930_164018/2_B01/bc1012_BAK8A_OA--bc1012_BAK8A_OA/m64089e_221001_201630.hifi_reads.bc1012_BAK8A_OA--bc1012_BAK8A_OA.bam.pbi
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.ccs_reports.json
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.ccs_reports.txt
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.consensusreadset.xml
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.primary_qc.tar.xz
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.reads.bam
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.reads.bam.pbi
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.sts.xml
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.subreads.bam
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.subreads.bam.pbi
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.transferdone
-t/data/pacbio/sequel/r64094e_20221214_160714/1_A01/m64094e_221214_161800.zmw_metrics.json.gz
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+t/data/pacbio/analysis/0000020083/outputs/sample2.transcripts.cluster_report.csv
+t/data/pacbio/analysis/0000020083/outputs/sample2.transcripts.fl_counts.csv
+t/data/pacbio/analysis/0000020083/outputs/sample3.transcripts.cluster_report.csv
+t/data/pacbio/analysis/0000020083/outputs/sample3.transcripts.fl_counts.csv
+t/data/pacbio/analysis/0000020083/outputs/sample4.transcripts.cluster_report.csv
+t/data/pacbio/analysis/0000020083/outputs/sample4.transcripts.fl_counts.csv
+t/data/pacbio/analysis/0000020083/outputs/segmented.bam
+t/data/pacbio/analysis/0000020083/outputs/segmented.consensusreadset.xml
+t/data/pacbio/analysis/0000020083/outputs/segmented.non_passing.bam
+t/data/pacbio/analysis/0000020083/outputs/transcripts-1.fasta
+t/data/pacbio/analysis/0000020083/outputs/transcripts-2.fasta
+t/data/pacbio/analysis/0000020083/outputs/transcripts-3.fasta
+t/data/pacbio/analysis/0000020083/outputs/transcripts-4.fasta
+t/data/pacbio/analysis/0000020083/outputs/transcripts-5.fasta
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.fasta
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.fl_count.txt
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.flnc_count.txt
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.gff
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.group.txt
+t/data/pacbio/analysis/0000020156/outputs/collapse_isoforms.read_stat.txt
+t/data/pacbio/analysis/0000020156/outputs/flnc-1.bam
+t/data/pacbio/analysis/0000020156/outputs/flnc-2.bam
+t/data/pacbio/analysis/0000020156/outputs/flnc-3.bam
+t/data/pacbio/analysis/0000020156/outputs/flnc-4.bam
+t/data/pacbio/analysis/0000020156/outputs/flnc-5.bam
+t/data/pacbio/analysis/0000020156/outputs/flnc.report-1.csv
+t/data/pacbio/analysis/0000020156/outputs/flnc.report-2.csv
+t/data/pacbio/analysis/0000020156/outputs/flnc.report-3.csv
+t/data/pacbio/analysis/0000020156/outputs/flnc.report-4.csv
+t/data/pacbio/analysis/0000020156/outputs/flnc.report-5.csv
+t/data/pacbio/analysis/0000020156/outputs/isoseq_mapping.report.json
+t/data/pacbio/analysis/0000020156/outputs/isoseq_primers.report.json
+t/data/pacbio/analysis/0000020156/outputs/isoseq.report.json
+t/data/pacbio/analysis/0000020156/outputs/mapped.bam
+t/data/pacbio/analysis/0000020156/outputs/mapped.bam.bai
+t/data/pacbio/analysis/0000020156/outputs/read_segmentation.report.json
+t/data/pacbio/analysis/0000020156/outputs/sample0.transcripts.cluster_report.csv
+t/data/pacbio/analysis/0000020156/outputs/sample0.transcripts.fl_counts.csv
+t/data/pacbio/analysis/0000020156/outputs/segmented.bam
+t/data/pacbio/analysis/0000020156/outputs/segmented.consensusreadset.xml
+t/data/pacbio/analysis/0000020156/outputs/segmented.non_passing.bam
+t/data/pacbio/analysis/0000020156/outputs/transcripts.fasta
 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
@@ -16837,18 +16836,18 @@ t/lib/WTSI/NPG/HTS/Illumina/LogPublisherTest.pm
 t/lib/WTSI/NPG/HTS/Illumina/MetaUpdaterTest.pm
 t/lib/WTSI/NPG/HTS/Illumina/RunPublisherTest.pm
 t/lib/WTSI/NPG/HTS/LIMSFactoryTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitorTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/AnalysisReportTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/ImageArchiveTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisherTest.pm
 t/lib/WTSI/NPG/HTS/PacBio/MetaUpdaterTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/RunAuditorTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitorTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/RunDeleteTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/RunMonitorTest.pm
+t/lib/WTSI/NPG/HTS/PacBio/RunPublisherTest.pm
 t/lib/WTSI/NPG/HTS/PacBio/SeqDataObjectTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReportTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchiveTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisherTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditorTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitorTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitorTest.pm
-t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm
 t/lib/WTSI/NPG/HTS/SeqchksumTest.pm
 t/lib/WTSI/NPG/HTS/Test.pm
 t/lib/WTSI/NPG/HTS/TreePublisherTest.pm
@@ -16859,18 +16858,18 @@ t/lib/WTSI/NPG/OM/BioNano/RunPublisherTest.pm
 t/lib/WTSI/NPG/OM/BioNano/Saphyr/RunPublisherTest.pm
 t/log_publisher.t
 t/location_writer.t
+t/pacbio_analysis_monitor.t
+t/pacbio_analysis_publisher.t
+t/pacbio_analysis_report.t
+t/pacbio_image_archive.t
+t/pacbio_isoseq_publisher.t
 t/pacbio_meta_updater.t
+t/pacbio_run_auditor.t
+t/pacbio_run_delete_monitor.t
+t/pacbio_run_delete.t
+t/pacbio_run_monitor.t
+t/pacbio_run_publisher.t
 t/pacbio_seq_data_object.t
-t/pacbio_sequel_analysis_monitor.t
-t/pacbio_sequel_analysis_publisher.t
-t/pacbio_sequel_analysis_report.t
-t/pacbio_sequel_image_archive.t
-t/pacbio_sequel_isoseq_publisher.t
-t/pacbio_sequel_run_auditor.t
-t/pacbio_sequel_run_delete_monitor.t
-t/pacbio_sequel_run_delete.t
-t/pacbio_sequel_run_monitor.t
-t/pacbio_sequel_run_publisher.t
 t/params.t
 t/perlcriticrc
 t/README
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm b/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm
similarity index 92%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm
rename to lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm
index df6e5685..e72c77b6 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitor.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitor.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor;
+package WTSI::NPG::HTS::PacBio::AnalysisMonitor;
 
 use namespace::autoclean;
 use DateTime;
@@ -8,13 +8,12 @@ use MooseX::StrictConstructor;
 use Readonly;
 use Try::Tiny;
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
-use WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher;
+use WTSI::NPG::HTS::PacBio::AnalysisPublisher;
+use WTSI::NPG::HTS::PacBio::IsoSeqPublisher;
 
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
        ];
 
 our $VERSION = '';
@@ -122,7 +121,7 @@ sub _publish_analysis_path {
     push @init_args, dest_collection => $self->dest_collection;
   }
 
-  my $publisher = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new(@init_args);
+  my $publisher = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new(@init_args);
 
   return $publisher->publish_files();
 }
@@ -145,7 +144,7 @@ sub _publish_iso_analysis_path {
 
   push @init_args, analysis_id => $job->{id};
 
-  my $publisher = WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher->new(@init_args);
+  my $publisher = WTSI::NPG::HTS::PacBio::IsoSeqPublisher->new(@init_args);
 
   return $publisher->publish_files();
 }
@@ -161,7 +160,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor
+WTSI::NPG::HTS::PacBio::AnalysisMonitor
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm
similarity index 96%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm
rename to lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm
index 91d26383..93f7b209 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisher.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisher.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
+package WTSI::NPG::HTS::PacBio::AnalysisPublisher;
 
 use namespace::autoclean;
 use English qw[-no_match_vars];
@@ -10,9 +10,9 @@ use MooseX::StrictConstructor;
 use Perl6::Slurp;
 use Readonly;
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::AnalysisReport;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::Product;
 
 with qw[
          WTSI::NPG::HTS::PacBio::PublisherBase
@@ -46,7 +46,7 @@ Readonly::Scalar my $HUNDRED       => 100;
 Readonly::Scalar my $MIN_BARCODED  => 0.8;
 Readonly::Scalar my $BARCODE_FIELD => 'Percent Barcoded Reads';
 Readonly::Scalar my $REPORT_TITLE  =>
-  $WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport::REPORTS;
+  $WTSI::NPG::HTS::PacBio::AnalysisReport::REPORTS;
 Readonly::Scalar my $LIMA_SUMMARY  => 'lima.summary.txt';
 
 
@@ -138,7 +138,7 @@ sub publish_sequence_files {
 
   my ($num_files, $num_processed, $num_errors) = (0, 0, 0);
 
-  my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+  my $product = WTSI::NPG::HTS::PacBio::Product->new();
 
   foreach my $file ( @{$files} ){
     my @tag_records;
@@ -318,7 +318,7 @@ sub _build_merged_report {
                    runfolder_path => $self->runfolder_path,
                    meta_data      => $self->_metadata);
 
-  my $report = WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport->new(@init_args);
+  my $report = WTSI::NPG::HTS::PacBio::AnalysisReport->new(@init_args);
   return $report->generate_analysis_report;
 }
 
@@ -422,7 +422,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher
+WTSI::NPG::HTS::PacBio::AnalysisPublisher
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm b/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
index 74e52dc2..23cffd99 100644
--- a/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherBase.pm
@@ -4,7 +4,7 @@ use File::Spec::Functions qw[catdir];
 use Moose::Role;
 use MooseX::StrictConstructor;
 use WTSI::NPG::HTS::PacBio::Metadata;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 our $VERSION = '';
 
@@ -55,7 +55,7 @@ sub _build_metadata{
     $self->logcroak('Metadata files is not defined for '. $self->analysis_path);
   }
 
-  return  WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+  return  WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
                  ($self->_metadata_file, $METADATA_PREFIX);
 }
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReport.pm b/lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm
similarity index 95%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReport.pm
rename to lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm
index d24412ff..8913e073 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReport.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/AnalysisReport.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport;
+package WTSI::NPG::HTS::PacBio::AnalysisReport;
 
 use namespace::autoclean;
 use File::Basename;
@@ -11,7 +11,7 @@ use Perl6::Slurp;
 use Readonly;
 use XML::LibXML;
 
-use WTSI::NPG::HTS::PacBio::Sequel::Reportdata;
+use WTSI::NPG::HTS::PacBio::Reportdata;
 
 with qw[
          WTSI::DNAP::Utilities::Loggable
@@ -147,7 +147,7 @@ sub _save_results {
     %files = map { $_ => $self->_get_result($_) } $self->_get_result_keys;
   }
 
-  my $data = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->new
+  my $data = WTSI::NPG::HTS::PacBio::Reportdata->new
     (meta_data => $self->meta_data,
      $REPORTS  => \%files );
 
@@ -169,7 +169,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport
+WTSI::NPG::HTS::PacBio::AnalysisReport
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm b/lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm
similarity index 98%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm
rename to lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm
index 95475583..9e661684 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchive.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/ImageArchive.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::ImageArchive;
+package WTSI::NPG::HTS::PacBio::ImageArchive;
 
 use namespace::autoclean;
 use File::Basename;
@@ -168,7 +168,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::ImageArchive
+WTSI::NPG::HTS::PacBio::ImageArchive
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm
similarity index 97%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm
rename to lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm
index 270d541e..3b91a687 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisher.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisher.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher;
+package WTSI::NPG::HTS::PacBio::IsoSeqPublisher;
 
 use namespace::autoclean;
 use DateTime;
@@ -15,8 +15,8 @@ use Readonly;
 use Try::Tiny;
 use XML::LibXML;
 
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::Product;
 use WTSI::DNAP::Utilities::Runnable;
 
 with qw[
@@ -197,7 +197,7 @@ sub publish_sequence_files {
 
   my ($num_files, $num_processed, $num_errors) = (0, 0, 0);
 
-  my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+  my $product = WTSI::NPG::HTS::PacBio::Product->new();
 
   foreach my $file ( @{$files} ){
 
@@ -368,7 +368,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher
+WTSI::NPG::HTS::PacBio::IsoSeqPublisher
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm b/lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm
similarity index 98%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm
rename to lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm
index 5f8fa26f..85da3300 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/MetaXMLParser.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/MetaXMLParser.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+package WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 use namespace::autoclean;
 use Moose;
@@ -145,7 +145,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser
+WTSI::NPG::HTS::PacBio::MetaXMLParser
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm b/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
index 5483d676..fb934917 100644
--- a/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/MonitorBase.pm
@@ -33,6 +33,36 @@ has 'mlwh_schema' =>
    required      => 1,
    documentation => 'A ML warehouse handle to obtain secondary metadata');
 
+has 'api_client' =>
+  (isa           => 'WTSI::NPG::HTS::PacBio::Sequel::APIClient',
+   is            => 'ro',
+   lazy_build    => 1,
+   builder       => q[_build_api_client],
+   documentation => 'A PacBio Sequel API client used to fetch runs');
+
+sub _build_api_client {
+    my $self = shift;
+    my @init_args = $self->api_uri ? ('api_uri' => $self->api_uri) : ();
+    if($self->interval) { push @init_args, ('default_interval' => $self->interval) };
+    if($self->older_than) { push @init_args, ('default_end' => $self->older_than) };
+    return WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(@init_args);
+}
+
+has 'api_uri' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'PacBio root API URL');
+
+has 'interval' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'Interval of time in days');
+
+has 'older_than' =>
+  (isa           => 'Str',
+   is            => 'ro',
+   documentation => 'Time in days to remove from end date');
+
 
 no Moose::Role;
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm b/lib/WTSI/NPG/HTS/PacBio/Product.pm
similarity index 96%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm
rename to lib/WTSI/NPG/HTS/PacBio/Product.pm
index a26daef4..abc2ef97 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/Product.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/Product.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::Product;
+package WTSI::NPG::HTS::PacBio::Product;
 
 use Moose;
 use English qw[-no_match_vars];
@@ -76,7 +76,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::Product
+WTSI::NPG::HTS::PacBio::Product
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm b/lib/WTSI/NPG/HTS/PacBio/Reportdata.pm
similarity index 95%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm
rename to lib/WTSI/NPG/HTS/PacBio/Reportdata.pm
index fb1a82de..af6f0164 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/Reportdata.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/Reportdata.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::Reportdata;
+package WTSI::NPG::HTS::PacBio::Reportdata;
 
 use namespace::autoclean;
 use DateTime;
@@ -60,7 +60,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::Reportdata
+WTSI::NPG::HTS::PacBio::Reportdata
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm b/lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm
similarity index 96%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm
index 9f95a059..fa991b16 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditor.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunAuditor.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunAuditor;
+package WTSI::NPG::HTS::PacBio::RunAuditor;
 
 use namespace::autoclean;
 use English qw[-no_match_vars];
@@ -17,8 +17,7 @@ Readonly::Scalar my $MODE_GROUP_WRITABLE => 0020;
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase
+         WTSI::NPG::HTS::PacBio::RunPublisherBase
        ];
 
 our $VERSION = '';
@@ -184,7 +183,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunAuditor
+WTSI::NPG::HTS::PacBio::RunAuditor
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm b/lib/WTSI/NPG/HTS/PacBio/RunDelete.pm
similarity index 95%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunDelete.pm
index 68936c54..4b475b8d 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDelete.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunDelete.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunDelete;
+package WTSI::NPG::HTS::PacBio::RunDelete;
 
 use namespace::autoclean;
 use Moose;
@@ -61,7 +61,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunDelete
+WTSI::NPG::HTS::PacBio::RunDelete
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitor.pm b/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitor.pm
similarity index 90%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitor.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitor.pm
index 94447e15..0b33d1e9 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitor.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitor.pm
@@ -1,17 +1,16 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor;
+package WTSI::NPG::HTS::PacBio::RunDeleteMonitor;
 
 use namespace::autoclean;
 use Moose;
 use MooseX::StrictConstructor;
 use Try::Tiny;
 
-use WTSI::NPG::HTS::PacBio::Sequel::RunDelete;
+use WTSI::NPG::HTS::PacBio::RunDelete;
 
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase
+         WTSI::NPG::HTS::PacBio::RunPublisherBase
        ];
 
 our $VERSION = '';
@@ -97,7 +96,7 @@ sub _delete_runfolder_path {
 
   my @init_args = (runfolder_path => $runfolder_path,);
 
-  my $deleter = WTSI::NPG::HTS::PacBio::Sequel::RunDelete->new(@init_args);
+  my $deleter = WTSI::NPG::HTS::PacBio::RunDelete->new(@init_args);
   return $deleter->delete_run($self->check_format);
 }
 
@@ -111,7 +110,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor
+WTSI::NPG::HTS::PacBio::RunDeleteMonitor
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitor.pm b/lib/WTSI/NPG/HTS/PacBio/RunMonitor.pm
similarity index 93%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitor.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunMonitor.pm
index ff4600a8..c30d1cc8 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitor.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunMonitor.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
+package WTSI::NPG::HTS::PacBio::RunMonitor;
 
 use namespace::autoclean;
 use Data::Dump qw[pp];
@@ -10,8 +10,7 @@ use Try::Tiny;
 with qw[
          WTSI::DNAP::Utilities::Loggable
          WTSI::NPG::HTS::PacBio::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
-         WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase
+         WTSI::NPG::HTS::PacBio::RunPublisherBase
        ];
 
 our $VERSION = '';
@@ -83,7 +82,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunMonitor
+WTSI::NPG::HTS::PacBio::RunMonitor
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm b/lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm
similarity index 97%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm
index 343f54a9..0a5913b0 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisher.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunPublisher.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
+package WTSI::NPG::HTS::PacBio::RunPublisher;
 
 use namespace::autoclean;
 use Data::Dump qw[pp];
@@ -11,10 +11,10 @@ use MooseX::StrictConstructor;
 use Readonly;
 use Try::Tiny;
 
-use WTSI::NPG::HTS::PacBio::Sequel::ImageArchive;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::ImageArchive;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::AnalysisPublisher;
+use WTSI::NPG::HTS::PacBio::Product;
 
 with qw[
          WTSI::NPG::HTS::PacBio::PublisherBase
@@ -60,7 +60,7 @@ Readonly::Scalar my $PRIMARY_REPORT_COUNT   => 4;
 Readonly::Scalar my $SECONDARY_REPORT_COUNT => 2;
 Readonly::Scalar my $CCS_REPORT_COUNT       => 6;
 Readonly::Scalar my $DATA_LEVEL_TWO         =>
-  $WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher::DATA_LEVEL;
+  $WTSI::NPG::HTS::PacBio::AnalysisPublisher::DATA_LEVEL;
 
 Readonly::Scalar my $ANALYSIS_ONBOARD    => 1;
 Readonly::Scalar my $MODE_GROUP_WRITABLE => q(0020);
@@ -362,7 +362,7 @@ sub _publish_deplexed_files {
      dest_collection => $self->dest_collection);
 
   my $publisher =
-    WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new(@init_args);
+    WTSI::NPG::HTS::PacBio::AnalysisPublisher->new(@init_args);
 
   try {
     ($num_files, $num_processed, $num_errors) = $publisher->publish_files();
@@ -468,7 +468,7 @@ sub publish_sequence_files {
      ($metadata->execution_mode eq 'OffInstrument') ||
      @run_records > 1 || $is_r_and_d || $is_aux) ? 0 : 1;
 
-  my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+  my $product = WTSI::NPG::HTS::PacBio::Product->new();
 
   my $id_product = $product->generate_product_id(
       $metadata->run_name,
@@ -614,7 +614,7 @@ sub publish_image_archive {
         dataset_id   => $metadata->subreads_uuid,
         report_count => $PRIMARY_REPORT_COUNT,
         archive_name => $metadata->movie_name .q[.]. $DATA_LEVEL .q[_qc];
-      my $iap = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@p_init);
+      my $iap = WTSI::NPG::HTS::PacBio::ImageArchive->new(@p_init);
       push @i_handles, $iap;
 
       if ($metadata->has_ccsreads_uuid) {
@@ -624,7 +624,7 @@ sub publish_image_archive {
           dataset_type => q[ccsreads],
           report_count => $SECONDARY_REPORT_COUNT,
           archive_name => $metadata->movie_name .q[.]. $DATA_LEVEL_TWO .q[_qc];
-        my $ias = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@s_init);
+        my $ias = WTSI::NPG::HTS::PacBio::ImageArchive->new(@s_init);
         push @i_handles, $ias;
       }
     }
@@ -673,7 +673,7 @@ sub publish_image_archive {
         report_count    => $CCS_REPORT_COUNT,
         archive_name    => $metadata->movie_name .q[.]. $DATA_LEVEL .q[_qc],
         specified_files => \@runfolder_files;
-      my $ias = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@s_init);
+      my $ias = WTSI::NPG::HTS::PacBio::ImageArchive->new(@s_init);
       push @i_handles, $ias;
     }
 
@@ -783,7 +783,7 @@ sub _read_metadata {
   $self->debug("Reading metadata from '$metadata_file'");
 
   my $metadata =
-    WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+    WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
       ($metadata_file,$prefix);
 
   return $metadata;
@@ -808,7 +808,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunPublisher
+WTSI::NPG::HTS::PacBio::RunPublisher
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherBase.pm b/lib/WTSI/NPG/HTS/PacBio/RunPublisherBase.pm
similarity index 94%
rename from lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherBase.pm
rename to lib/WTSI/NPG/HTS/PacBio/RunPublisherBase.pm
index 7f0c21e9..e0a7fcfb 100644
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherBase.pm
+++ b/lib/WTSI/NPG/HTS/PacBio/RunPublisherBase.pm
@@ -1,9 +1,9 @@
-package  WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase;
+package  WTSI::NPG::HTS::PacBio::RunPublisherBase;
 
 use Moose::Role;
 use File::Spec::Functions qw[canonpath catdir];
 
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
+use WTSI::NPG::HTS::PacBio::RunPublisher;
 
 Readonly::Scalar my $PROD_DIR_COUNT     => 5;
 Readonly::Scalar my $NEW_PROD_DIR_COUNT => 6;
@@ -20,7 +20,7 @@ our $VERSION = '';
   Arg [1]    : runfolder path
   Example    : my $publisher = $self->run_publisher_handle($runfolder_path);
   Description: publisher handle for a specific runfolder
-  Returntype : WTSI::NPG::HTS::PacBio::Sequel::RunPublisher
+  Returntype : WTSI::NPG::HTS::PacBio::RunPublisher
 
 =cut
 
@@ -41,7 +41,7 @@ sub run_publisher_handle {
     if ($self->dest_collection) {
         push @init_args, dest_collection => $self->dest_collection;
     }
-    my $publisher = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new(@init_args);
+    my $publisher = WTSI::NPG::HTS::PacBio::RunPublisher->new(@init_args);
 
     return $publisher;
 }
@@ -168,7 +168,7 @@ __END__
 
 =head1 NAME
 
-WTSI::NPG::HTS::PacBio::Sequel::RunPublisherBase
+WTSI::NPG::HTS::PacBio::RunPublisherBase
 
 =head1 DESCRIPTION
 
diff --git a/lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm b/lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm
deleted file mode 100644
index 3feec604..00000000
--- a/lib/WTSI/NPG/HTS/PacBio/Sequel/MonitorBase.pm
+++ /dev/null
@@ -1,69 +0,0 @@
-package WTSI::NPG::HTS::PacBio::Sequel::MonitorBase;
-
-use Moose::Role;
-use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-
-our $VERSION = '';
-
-has 'api_client' =>
-  (isa           => 'WTSI::NPG::HTS::PacBio::Sequel::APIClient',
-   is            => 'ro',
-   lazy_build    => 1,
-   builder       => q[_build_api_client],
-   documentation => 'A PacBio Sequel API client used to fetch runs');
-
-sub _build_api_client {
-    my $self = shift;
-    my @init_args = $self->api_uri ? ('api_uri' => $self->api_uri) : ();
-    if($self->interval) { push @init_args, ('default_interval' => $self->interval) };
-    if($self->older_than) { push @init_args, ('default_end' => $self->older_than) };
-    return WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(@init_args);
-}
-
-has 'api_uri' =>
-  (isa           => 'Str',
-   is            => 'ro',
-   documentation => 'PacBio root API URL');
-
-has 'interval' =>
-  (isa           => 'Str',
-   is            => 'ro',
-   documentation => 'Interval of time in days');
-
-has 'older_than' =>
-  (isa           => 'Str',
-   is            => 'ro',
-   documentation => 'Time in days to remove from end date');
-
-no Moose::Role;
-
-1;
-
-__END__
-
-
-=head1 NAME
-
-WTSI::NPG::HTS::PacBio::Sequel::MonitorBase
-
-=head1 DESCRIPTION
-
-Base for Sequel Monitors.
-
-=head1 AUTHOR
-
-=head1 COPYRIGHT AND DISCLAIMER
-
-Copyright (C) 2019 Genome Research Limited. All Rights Reserved.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the Perl Artistic License or 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.
-
-=cut
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam.pbi
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.bam.pbi
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.consensusreadset.xml
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.bc1018_BAK8B_OA--bc1018_BAK8B_OA.consensusreadset.xml
diff --git a/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.counts b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.counts
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.counts
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.counts
diff --git a/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.guess.txt b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.guess.txt
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.guess.txt
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.guess.txt
diff --git a/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.summary.txt b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.summary.txt
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.summary.txt
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.lima.summary.txt
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam.pbi
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.bam.pbi
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.consensusreadset.xml
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam
rename to t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/demultiplex.removed.consensusreadset.xml
diff --git a/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
new file mode 100644
index 00000000..3d268e99
--- /dev/null
+++ b/t/data/pacbio/analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
@@ -0,0 +1 @@
+{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2020-12-28T21:07:04","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","cell_index":"0","collection_number":"0","ccsreads_uuid":"358e948d-d467-4e68-b5b0-a35b5def1a3f","execution_mode":"None","file_path":"t/data/pacbio/analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml","instrument_name":"64016","movie_name":"m64016_201030_125711","results_folder":"r64016_20201030_121742/1_A01/","run_name":"78039","sample_load_name":"DN678359V-H1","subreads_uuid":"7da072af-387d-49e8-8ee3-b0fa0c873fb7","ts_run_name":"r64016_20201030_121742","version_info":{"chemistry":"9.0.0.92017","ics":"9.0.0.92233","iui":"9.0.0.92233","pa":"9.0.0.92233","paws":"9.0.0.92233","ppa":"9.0.0.92233","realtime":"9.0.0.92233","smrtimisc":"9.0.0.92188","smrtinub":"9.0.0.92188","smrtlink":"9.0.0.92188","smrtlink-analysisservices-gui":"9.0.0.92188","smrttools":"9.0.0.92188","transfer":"9.0.0.92233"},"well_name":"A01"},"reports":{"barcode_ccs.report.json":[{"id":"barcode.n_barcodes","name":"Unique Barcodes","value":1},{"id":"barcode.n_barcoded_reads","name":"Barcoded Reads","value":1810026},{"id":"barcode.mean_reads","name":"Mean Reads","value":1810026},{"id":"barcode.max_reads","name":"Max. Reads","value":1810026},{"id":"barcode.min_reads","name":"Min. Reads","value":1810026},{"id":"barcode.mean_read_length","name":"Mean Read Length","value":12395},{"id":"barcode.n_unbarcoded_reads","name":"Unbarcoded Reads","value":3953},{"id":"barcode.percent_barcoded_bases","name":"Percent Bases in Barcoded Reads","value":0.997885957315498},{"id":"barcode.percent_barcoded_reads","name":"Percent Barcoded Reads","value":0.997820812699596}],"ccs.report.json":[{"id":"ccs2.number_of_ccs_reads","name":"HiFi Reads","value":1813979},{"id":"ccs2.total_number_of_ccs_bases","name":"HiFi Yield (bp)","value":22540634412},{"id":"ccs2.mean_ccs_readlength","name":"HiFi Read Length (mean, bp)","value":12426},{"id":"ccs2.median_accuracy","name":"HiFi Read Quality (median)","value":"Q31"},{"id":"ccs2.mean_npasses","name":"HiFi Number of Passes (mean)","value":11},{"id":"ccs2.n_low_quality_reads","name":"<Q20 Reads","value":360373},{"id":"ccs2.total_number_of_ccs_bases_lq","name":"<Q20 Yield (bp)","value":5134415371},{"id":"ccs2.mean_ccs_readlength_lq","name":"<Q20 Read Length (mean, bp)","value":14247},{"id":"ccs2.median_accuracy_lq","name":"<Q20 Read Quality (median)","value":"Q16"}],"ccs_processing.report.json":[{"id":"ccs_processing.zmw_input","name":"ZMWs input","value":5115474},{"id":"ccs_processing.zmw_passed_yield","name":"ZMWs pass filters","value":2174352},{"id":"ccs_processing.zmw_filtered_yield","name":"ZMWs fail filters","value":2941122},{"id":"ccs_processing.zmw_2_pass_shortcut","name":"ZMWs shortcut filters","value":2629808},{"id":"ccs_processing.zmw_tandem_repeat","name":"ZMWs with tandem repeats","value":15780},{"id":"ccs_processing.filtered_poor_snr","name":"Below SNR threshold","value":72970},{"id":"ccs_processing.filtered_median_length_filter","name":"Median length filter","value":0},{"id":"ccs_processing.filtered_too_few_passes","name":"Lacking full passes","value":0},{"id":"ccs_processing.filtered_heteroduplexes","name":"Heteroduplex insertions","value":40722},{"id":"ccs_processing.filtered_coverage_drops","name":"Coverage drops","value":103369},{"id":"ccs_processing.filtered_insufficient_draft_cov","name":"Insufficient draft cov","value":71328},{"id":"ccs_processing.filtered_draft_too_different","name":"Draft too different","value":0},{"id":"ccs_processing.filtered_draft_failure","name":"Draft generation error","value":10276},{"id":"ccs_processing.filtered_draft_too_long","name":"Draft above --max-length","value":0},{"id":"ccs_processing.filtered_draft_too_short","name":"Draft below --min-length","value":0},{"id":"ccs_processing.filtered_read_failed_polish","name":"Reads failed polishing","value":5},{"id":"ccs_processing.filtered_empty_window_during_polishing","name":"Empty coverage windows","value":12246},{"id":"ccs_processing.filtered_non_convergent","name":"CCS did not converge","value":398},{"id":"ccs_processing.filtered_below_rq","name":"CCS below minimum RQ","value":0},{"id":"ccs_processing.filtered_unknown_error","name":"Unknown error","value":0}],"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n11\t11\tbc1018_BAK8B_OA\tbc1018_BAK8B_OA\t1810026\t90\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n0\t0\tbc1001_BAK8A_OA\tbc1001_BAK8A_OA\t1\t23\t0\n1\t1\tbc1002_BAK8A_OA\tbc1002_BAK8A_OA\t3\t23\t0\n2\t2\tbc1003_BAK8A_OA\tbc1003_BAK8A_OA\t2\t18\t0\n3\t3\tbc1008_BAK8A_OA\tbc1008_BAK8A_OA\t3\t21\t0\n4\t4\tbc1009_BAK8A_OA\tbc1009_BAK8A_OA\t2\t24\t0\n5\t5\tbc1010_BAK8A_OA\tbc1010_BAK8A_OA\t1\t35\t0\n6\t6\tbc1011_BAK8A_OA\tbc1011_BAK8A_OA\t2\t18\t0\n7\t7\tbc1012_BAK8A_OA\tbc1012_BAK8A_OA\t3\t22\t0\n8\t8\tbc1015_BAK8B_OA\tbc1015_BAK8B_OA\t1\t17\t0\n9\t9\tbc1016_BAK8B_OA\tbc1016_BAK8B_OA\t3\t20\t0\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t1\t23\t0\n11\t11\tbc1018_BAK8B_OA\tbc1018_BAK8B_OA\t48699\t85\t1\n12\t12\tbc1019_BAK8B_OA\tbc1019_BAK8B_OA\t2\t27\t0\n14\t14\tbc1021_BAK8B_OA\tbc1021_BAK8B_OA\t3\t22\t0\n15\t15\tbc1022_BAK8B_OA\tbc1022_BAK8B_OA\t2\t15\t0\n","demultiplex.lima.summary.txt":"ZMWs input                (A) : 1813979\nZMWs above all thresholds (B) : 1810026 (100%)\nZMWs below any threshold  (C) : 3953 (0%)\n\nZMW marginals for (C):\nBelow min length              : 91 (2%)\nBelow min score               : 107 (3%)\nBelow min end score           : 107 (3%)\nBelow min passes              : 0 (0%)\nBelow min score lead          : 107 (3%)\nBelow min ref span            : 3865 (98%)\nWithout SMRTbell adapter      : 0 (0%)\n\nZMWs for (B):\nWith same pair                : 1810026 (100%)\nCoefficient of correlation    : 0%\n\nZMWs for (A):\nAllow diff pair               : 1813979 (100%)\nAllow same pair               : 1813979 (100%)\n\nReads for (B):\nAbove length                  : 1810026 (100%)\nBelow length                  : 0 (0%)\n"}}
diff --git a/t/data/pacbio/sequel_analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml b/t/data/pacbio/analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml
rename to t/data/pacbio/analysis/0000002152/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml
diff --git a/t/data/pacbio/sequel_analysis/0000002152/outputs/barcode_ccs.report.json b/t/data/pacbio/analysis/0000002152/outputs/barcode_ccs.report.json
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rename from t/data/pacbio/sequel_analysis/0000002152/outputs/barcode_ccs.report.json
rename to t/data/pacbio/analysis/0000002152/outputs/barcode_ccs.report.json
diff --git a/t/data/pacbio/sequel_analysis/0000002152/outputs/ccs.report.json b/t/data/pacbio/analysis/0000002152/outputs/ccs.report.json
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rename from t/data/pacbio/sequel_analysis/0000002152/outputs/ccs.report.json
rename to t/data/pacbio/analysis/0000002152/outputs/ccs.report.json
diff --git a/t/data/pacbio/sequel_analysis/0000002152/outputs/ccs_processing.report.json b/t/data/pacbio/analysis/0000002152/outputs/ccs_processing.report.json
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rename from t/data/pacbio/sequel_analysis/0000002152/outputs/ccs_processing.report.json
rename to t/data/pacbio/analysis/0000002152/outputs/ccs_processing.report.json
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam
similarity index 100%
rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam
diff --git a/t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.transferdone b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi
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rename from t/data/pacbio/sequel/r54097_20170727_165601/1_A02/m54097_170727_170646.transferdone
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.bam.pbi
diff --git a/t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml
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rename from t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.bc1017_BAK8B_OA--bc1017_BAK8B_OA.consensusreadset.xml
diff --git a/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.counts
diff --git a/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.guess.txt
diff --git a/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt
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rename from t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.lima.summary.txt
diff --git a/t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam.pbi b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam
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rename from t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/bc1015_BAK8B_OA--bc1015_BAK8B_OA/m64089e_220615_173331.hifi_reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.bam.pbi
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam
diff --git a/t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.baz2bam_1.log b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi
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rename from t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.baz2bam_1.log
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.bam.pbi
diff --git a/t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs.log b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml
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rename from t/data/pacbio/sequel/r64089e_20220615_171559/1_A01/m64089e_220615_173331.ccs.log
rename to t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/demultiplex.removed.consensusreadset.xml
diff --git a/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
new file mode 100644
index 00000000..d7837674
--- /dev/null
+++ b/t/data/pacbio/analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
@@ -0,0 +1 @@
+{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata-2.28.0","created_at":"2021-04-24T07:30:04","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata-2.28.0","ccsreads_uuid":"a8ddfa78-f166-4547-ada4-72bd46f608af","cell_index":"1","collection_number":"1","execution_mode":"OffInstrument","file_path":"t/data/pacbio/analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml","instrument_name":"64221E","movie_name":"m64221e_210410_143943","results_folder":"r64221e_20210409_135810/2_B01/","run_name":"81230","sample_load_name":"DN787408U-C2","subreads_uuid":"081746ec-5099-4efb-9702-0f97bf22dc59","ts_run_name":"r64221e_20210409_135810","version_info":{"chemistry":"10.0.0.108341","ics":"10.0.0.111772","iui":"10.0.0.111772","pa":"10.0.0.111772","paws":"10.0.0.111772","ppa":"10.0.0.111772","realtime":"10.0.0.111772","smrtimisc":"10.0.0.108728","smrtinub":"10.0.0.108728","smrtlink":"10.0.0.108728","smrtlink-analysisservices-gui":"10.0.0.108728","smrttools":"10.0.0.108728","transfer":"10.0.0.111772"},"well_name":"B01"},"reports":{"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t80042\t95\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n3\t3\tbc1008_BAK8A_OA\tbc1008_BAK8A_OA\t3\t71\t0\n4\t4\tbc1009_BAK8A_OA\tbc1009_BAK8A_OA\t1\t28\t0\n5\t5\tbc1010_BAK8A_OA\tbc1010_BAK8A_OA\t1\t29\t0\n6\t6\tbc1011_BAK8A_OA\tbc1011_BAK8A_OA\t3\t24\t0\n7\t7\tbc1012_BAK8A_OA\tbc1012_BAK8A_OA\t5\t79\t0\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t49385\t89\t1\n14\t14\tbc1021_BAK8B_OA\tbc1021_BAK8B_OA\t1\t17\t0\n15\t15\tbc1022_BAK8B_OA\tbc1022_BAK8B_OA\t1\t100\t0\n","demultiplex.lima.summary.txt":"ZMWs input                (A) : 80139\nZMWs above all thresholds (B) : 80042 (100%)\nZMWs below any threshold  (C) : 97 (0%)\n\nZMW marginals for (C):\nBelow min length              : 15 (15%)\nBelow min score               : 34 (35%)\nBelow min end score           : 34 (35%)\nBelow min passes              : 0 (0%)\nBelow min score lead          : 34 (35%)\nBelow min ref span            : 82 (85%)\nWithout SMRTbell adapter      : 0 (0%)\n\nZMWs for (B):\nWith same pair                : 80042 (100%)\nCoefficient of correlation    : 0%\n\nZMWs for (A):\nAllow diff pair               : 80139 (100%)\nAllow same pair               : 80139 (100%)\n\nReads for (B):\nAbove length                  : 80042 (100%)\nBelow length                  : 0 (0%)\n"}}
diff --git a/t/data/pacbio/sequel_analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml b/t/data/pacbio/analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml
rename to t/data/pacbio/analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml
diff --git a/t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json b/t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json
rename to t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json
diff --git a/t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot.png b/t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot.png
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot.png
rename to t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot.png
diff --git a/t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot_thumb.png b/t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot_thumb.png
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot_thumb.png
rename to t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/concordance_plot_thumb.png
diff --git a/t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json b/t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json
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rename from t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json
rename to t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json
diff --git a/t/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/readlength_plot.png b/t/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/readlength_plot.png
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diff --git a/t/data/pacbio/sequel_analysis/0000003499/entry-points/2a711efd-0812-4a5f-b4a2-29714400611f.subreadset.xml b/t/data/pacbio/analysis/0000003499/entry-points/2a711efd-0812-4a5f-b4a2-29714400611f.subreadset.xml
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diff --git a/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml b/t/data/pacbio/analysis/0000019480/outputs/m84098_240322_112047_s1.bc2048--bc2048.consensusreadset.xml
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diff --git a/t/data/pacbio/sequel_analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml b/t/data/pacbio/analysis/0000019480/outputs/m84098_240322_112047_s1.consensusreadset.xml
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diff --git a/t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam b/t/data/pacbio/analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam
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diff --git a/t/data/pacbio/sequel/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam.pbi b/t/data/pacbio/analysis/0000019480_deplexfail/cromwell-job/call-lima/execution/bc2048--bc2048/m84098_240322_112047_s1.bc2048--bc2048.bam.pbi
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diff --git a/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
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--- a/t/data/pacbio/sequel_analysis/0000002152/cromwell-job/call-demultiplex_barcodes/demultiplex_barcodes/5df96c44/call-lima/execution/merged_analysis_report.json
+++ /dev/null
@@ -1 +0,0 @@
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Reads","value":1810026},{"id":"barcode.mean_read_length","name":"Mean Read Length","value":12395},{"id":"barcode.n_unbarcoded_reads","name":"Unbarcoded Reads","value":3953},{"id":"barcode.percent_barcoded_bases","name":"Percent Bases in Barcoded Reads","value":0.997885957315498},{"id":"barcode.percent_barcoded_reads","name":"Percent Barcoded Reads","value":0.997820812699596}],"ccs.report.json":[{"id":"ccs2.number_of_ccs_reads","name":"HiFi Reads","value":1813979},{"id":"ccs2.total_number_of_ccs_bases","name":"HiFi Yield (bp)","value":22540634412},{"id":"ccs2.mean_ccs_readlength","name":"HiFi Read Length (mean, bp)","value":12426},{"id":"ccs2.median_accuracy","name":"HiFi Read Quality (median)","value":"Q31"},{"id":"ccs2.mean_npasses","name":"HiFi Number of Passes (mean)","value":11},{"id":"ccs2.n_low_quality_reads","name":"<Q20 Reads","value":360373},{"id":"ccs2.total_number_of_ccs_bases_lq","name":"<Q20 Yield (bp)","value":5134415371},{"id":"ccs2.mean_ccs_readlength_lq","name":"<Q20 Read Length (mean, bp)","value":14247},{"id":"ccs2.median_accuracy_lq","name":"<Q20 Read Quality (median)","value":"Q16"}],"ccs_processing.report.json":[{"id":"ccs_processing.zmw_input","name":"ZMWs input","value":5115474},{"id":"ccs_processing.zmw_passed_yield","name":"ZMWs pass filters","value":2174352},{"id":"ccs_processing.zmw_filtered_yield","name":"ZMWs fail filters","value":2941122},{"id":"ccs_processing.zmw_2_pass_shortcut","name":"ZMWs shortcut filters","value":2629808},{"id":"ccs_processing.zmw_tandem_repeat","name":"ZMWs with tandem repeats","value":15780},{"id":"ccs_processing.filtered_poor_snr","name":"Below SNR threshold","value":72970},{"id":"ccs_processing.filtered_median_length_filter","name":"Median length filter","value":0},{"id":"ccs_processing.filtered_too_few_passes","name":"Lacking full passes","value":0},{"id":"ccs_processing.filtered_heteroduplexes","name":"Heteroduplex insertions","value":40722},{"id":"ccs_processing.filtered_coverage_drops","name":"Coverage drops","value":103369},{"id":"ccs_processing.filtered_insufficient_draft_cov","name":"Insufficient draft cov","value":71328},{"id":"ccs_processing.filtered_draft_too_different","name":"Draft too different","value":0},{"id":"ccs_processing.filtered_draft_failure","name":"Draft generation error","value":10276},{"id":"ccs_processing.filtered_draft_too_long","name":"Draft above --max-length","value":0},{"id":"ccs_processing.filtered_draft_too_short","name":"Draft below --min-length","value":0},{"id":"ccs_processing.filtered_read_failed_polish","name":"Reads failed polishing","value":5},{"id":"ccs_processing.filtered_empty_window_during_polishing","name":"Empty coverage windows","value":12246},{"id":"ccs_processing.filtered_non_convergent","name":"CCS did not converge","value":398},{"id":"ccs_processing.filtered_below_rq","name":"CCS below minimum RQ","value":0},{"id":"ccs_processing.filtered_unknown_error","name":"Unknown error","value":0}],"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n11\t11\tbc1018_BAK8B_OA\tbc1018_BAK8B_OA\t1810026\t90\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n0\t0\tbc1001_BAK8A_OA\tbc1001_BAK8A_OA\t1\t23\t0\n1\t1\tbc1002_BAK8A_OA\tbc1002_BAK8A_OA\t3\t23\t0\n2\t2\tbc1003_BAK8A_OA\tbc1003_BAK8A_OA\t2\t18\t0\n3\t3\tbc1008_BAK8A_OA\tbc1008_BAK8A_OA\t3\t21\t0\n4\t4\tbc1009_BAK8A_OA\tbc1009_BAK8A_OA\t2\t24\t0\n5\t5\tbc1010_BAK8A_OA\tbc1010_BAK8A_OA\t1\t35\t0\n6\t6\tbc1011_BAK8A_OA\tbc1011_BAK8A_OA\t2\t18\t0\n7\t7\tbc1012_BAK8A_OA\tbc1012_BAK8A_OA\t3\t22\t0\n8\t8\tbc1015_BAK8B_OA\tbc1015_BAK8B_OA\t1\t17\t0\n9\t9\tbc1016_BAK8B_OA\tbc1016_BAK8B_OA\t3\t20\t0\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t1\t23\t0\n11\t11\tbc1018_BAK8B_OA\tbc1018_BAK8B_OA\t48699\t85\t1\n12\t12\tbc1019_BAK8B_OA\tbc1019_BAK8B_OA\t2\t27\t0\n14\t14\tbc1021_BAK8B_OA\tbc1021_BAK8B_OA\t3\t22\t0\n15\t15\tbc1022_BAK8B_OA\tbc1022_BAK8B_OA\t2\t15\t0\n","demultiplex.lima.summary.txt":"ZMWs input                (A) : 1813979\nZMWs above all thresholds (B) : 1810026 (100%)\nZMWs below any threshold  (C) : 3953 (0%)\n\nZMW marginals for (C):\nBelow min length              : 91 (2%)\nBelow min score               : 107 (3%)\nBelow min end score           : 107 (3%)\nBelow min passes              : 0 (0%)\nBelow min score lead          : 107 (3%)\nBelow min ref span            : 3865 (98%)\nWithout SMRTbell adapter      : 0 (0%)\n\nZMWs for (B):\nWith same pair                : 1810026 (100%)\nCoefficient of correlation    : 0%\n\nZMWs for (A):\nAllow diff pair               : 1813979 (100%)\nAllow same pair               : 1813979 (100%)\n\nReads for (B):\nAbove length                  : 1810026 (100%)\nBelow length                  : 0 (0%)\n"}}
diff --git a/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
deleted file mode 100644
index 68fe81d9..00000000
--- a/t/data/pacbio/sequel_analysis/0000003442/cromwell-job/call-demultiplex_barcodes/call-lima/execution/merged_analysis_report.json
+++ /dev/null
@@ -1 +0,0 @@
-{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata-2.28.0","created_at":"2021-04-24T07:30:04","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata-2.28.0","ccsreads_uuid":"a8ddfa78-f166-4547-ada4-72bd46f608af","cell_index":"1","collection_number":"1","execution_mode":"OffInstrument","file_path":"t/data/pacbio/sequel_analysis/0000003442/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml","instrument_name":"64221E","movie_name":"m64221e_210410_143943","results_folder":"r64221e_20210409_135810/2_B01/","run_name":"81230","sample_load_name":"DN787408U-C2","subreads_uuid":"081746ec-5099-4efb-9702-0f97bf22dc59","ts_run_name":"r64221e_20210409_135810","version_info":{"chemistry":"10.0.0.108341","ics":"10.0.0.111772","iui":"10.0.0.111772","pa":"10.0.0.111772","paws":"10.0.0.111772","ppa":"10.0.0.111772","realtime":"10.0.0.111772","smrtimisc":"10.0.0.108728","smrtinub":"10.0.0.108728","smrtlink":"10.0.0.108728","smrtlink-analysisservices-gui":"10.0.0.108728","smrttools":"10.0.0.108728","transfer":"10.0.0.111772"},"well_name":"B01"},"reports":{"demultiplex.lima.counts":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t80042\t95\n","demultiplex.lima.guess.txt":"IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tNumZMWs\tMeanScore\tPicked\n3\t3\tbc1008_BAK8A_OA\tbc1008_BAK8A_OA\t3\t71\t0\n4\t4\tbc1009_BAK8A_OA\tbc1009_BAK8A_OA\t1\t28\t0\n5\t5\tbc1010_BAK8A_OA\tbc1010_BAK8A_OA\t1\t29\t0\n6\t6\tbc1011_BAK8A_OA\tbc1011_BAK8A_OA\t3\t24\t0\n7\t7\tbc1012_BAK8A_OA\tbc1012_BAK8A_OA\t5\t79\t0\n10\t10\tbc1017_BAK8B_OA\tbc1017_BAK8B_OA\t49385\t89\t1\n14\t14\tbc1021_BAK8B_OA\tbc1021_BAK8B_OA\t1\t17\t0\n15\t15\tbc1022_BAK8B_OA\tbc1022_BAK8B_OA\t1\t100\t0\n","demultiplex.lima.summary.txt":"ZMWs input                (A) : 80139\nZMWs above all thresholds (B) : 80042 (100%)\nZMWs below any threshold  (C) : 97 (0%)\n\nZMW marginals for (C):\nBelow min length              : 15 (15%)\nBelow min score               : 34 (35%)\nBelow min end score           : 34 (35%)\nBelow min passes              : 0 (0%)\nBelow min score lead          : 34 (35%)\nBelow min ref span            : 82 (85%)\nWithout SMRTbell adapter      : 0 (0%)\n\nZMWs for (B):\nWith same pair                : 80042 (100%)\nCoefficient of correlation    : 0%\n\nZMWs for (A):\nAllow diff pair               : 80139 (100%)\nAllow same pair               : 80139 (100%)\n\nReads for (B):\nAbove length                  : 80042 (100%)\nBelow length                  : 0 (0%)\n"}}
diff --git a/t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/merged_analysis_report.json b/t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/merged_analysis_report.json
deleted file mode 100644
index d62470f5..00000000
--- a/t/data/pacbio/sequel_analysis/0000003499/cromwell-job/call-export_bam/execution/merged_analysis_report.json
+++ /dev/null
@@ -1 +0,0 @@
-{"__CLASS__":"WTSI::NPG::HTS::PacBio::Sequel::Reportdata","created_at":"2021-05-10T11:23:36","meta_data":{"__CLASS__":"WTSI::NPG::HTS::PacBio::Metadata","ccsreads_uuid":"c3bdd7a7-8db5-488c-98c4-2a0a5717f541","cell_index":"0","collection_number":"0","execution_mode":"OffInstrument","file_path":"t/data/pacbio/sequel_analysis/0000003499/entry-points/2a711efd-0812-4a5f-b4a2-29714400611f.subreadset.xml","instrument_name":"64089e","is_ccs":"true","movie_name":"m64089e_210429_170734","results_folder":"r64089e_20210429_165558/1_A01/","run_name":"81876","sample_load_name":"DN712146I-B1","subreads_uuid":"2a711efd-0812-4a5f-b4a2-29714400611f","ts_run_name":"r64089e_20210429_165558","version_info":{"chemistry":"10.1.0.115879","ics":"10.1.0.115920","iui":"10.1.0.115920","pa":"10.1.0.115920","paws":"10.1.0.115920","ppa":"10.1.0.115920","realtime":"10.1.0.115920","smrtimisc":"10.1.0.115913","smrtinub":"10.1.0.115913","smrtlink":"10.1.0.115913","smrtlink-analysisservices-gui":"10.1.0.115913","smrttools":"10.1.0.115913","transfer":"10.1.0.115920"},"well_name":"A01"},"reports":{"ccs.report.json":[{"id":"ccs2.number_of_ccs_reads","name":"HiFi Reads","value":1814937},{"id":"ccs2.total_number_of_ccs_bases","name":"HiFi Yield (bp)","value":26168023874},{"id":"ccs2.mean_ccs_readlength","name":"HiFi Read Length (mean, bp)","value":14418},{"id":"ccs2.median_accuracy","name":"HiFi Read Quality (median)","value":"Q32"},{"id":"ccs2.mean_npasses","name":"HiFi Number of Passes (mean)","value":11},{"id":"ccs2.n_low_quality_reads","name":"<Q20 Reads","value":314433},{"id":"ccs2.total_number_of_ccs_bases_lq","name":"<Q20 Yield (bp)","value":4751387627},{"id":"ccs2.mean_ccs_readlength_lq","name":"<Q20 Read Length (mean, bp)","value":15110},{"id":"ccs2.median_accuracy_lq","name":"<Q20 Read Quality (median)","value":"Q17"}],"ccs_processing.report.json":[{"id":"ccs_processing.zmw_input","name":"ZMWs input","value":6119323},{"id":"ccs_processing.zmw_passed_yield","name":"ZMWs pass filters","value":2129370},{"id":"ccs_processing.zmw_filtered_yield","name":"ZMWs fail filters","value":3989953},{"id":"ccs_processing.zmw_2_pass_shortcut","name":"ZMWs shortcut filters","value":3616276},{"id":"ccs_processing.zmw_tandem_repeat","name":"ZMWs with tandem repeats","value":21516},{"id":"ccs_processing.filtered_poor_snr","name":"Below SNR threshold","value":61991},{"id":"ccs_processing.filtered_median_length_filter","name":"Median length filter","value":0},{"id":"ccs_processing.filtered_too_few_passes","name":"Lacking full passes","value":0},{"id":"ccs_processing.filtered_heteroduplexes","name":"Heteroduplex insertions","value":42893},{"id":"ccs_processing.filtered_coverage_drops","name":"Coverage drops","value":8985},{"id":"ccs_processing.filtered_insufficient_draft_cov","name":"Insufficient draft cov","value":213139},{"id":"ccs_processing.filtered_draft_too_different","name":"Draft too different","value":0},{"id":"ccs_processing.filtered_draft_failure","name":"Draft generation error","value":43649},{"id":"ccs_processing.filtered_draft_too_long","name":"Draft above --max-length","value":0},{"id":"ccs_processing.filtered_draft_too_short","name":"Draft below --min-length","value":6},{"id":"ccs_processing.filtered_read_failed_polish","name":"Reads failed polishing","value":0},{"id":"ccs_processing.filtered_empty_window_during_polishing","name":"Empty coverage windows","value":1257},{"id":"ccs_processing.filtered_non_convergent","name":"CCS did not converge","value":1757},{"id":"ccs_processing.filtered_below_rq","name":"CCS below minimum RQ","value":0},{"id":"ccs_processing.filtered_unknown_error","name":"Unknown error","value":0}]}}
diff --git a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json b/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json
deleted file mode 100644
index fade3af0..00000000
--- a/t/data/pacbio/sequel_analysis/0000019480/cromwell-job/call-lima/execution/mlwh_locations.json
+++ /dev/null
@@ -1 +0,0 @@
-{"version":"1.0","products":[{"pipeline_name":"npg-prod","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.13951.0/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","seq_platform_name":"pacbio"},{"seq_platform_name":"pacbio","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.8865.0/1_A01/","pipeline_name":"npg-prod"},{"seq_platform_name":"pacbio","pipeline_name":"npg-prod","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.39705.0/1_A01/"},{"seq_platform_name":"pacbio","pipeline_name":"npg-prod","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.52268.0/1_A01/"},{"pipeline_name":"npg-prod","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.829372.0/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","seq_platform_name":"pacbio"},{"seq_platform_name":"pacbio","pipeline_name":"npg-prod","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.52482.0/1_A01/"},{"id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.54890.0/1_A01/","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","pipeline_name":"npg-prod","seq_platform_name":"pacbio"},{"irods_root_collection":"/Sanger1-dev/home/ces/AnalysisPublisherTest.660768.0/1_A01/","id_product":"04bd5036fff6b0037535221ba755725b14ef0f4f44a3ac0030f899edaae2e391","irods_data_relative_path":"m84098_240322_112047_s1.bc2048--bc2048.bam","pipeline_name":"npg-prod","seq_platform_name":"pacbio"}]}
\ No newline at end of file
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam.pbi b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.bc1010_BAK8A_OA.bam.pbi
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.adapters.fasta
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.primary_qc.tar.xz
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam.pbi b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/hifi_reads/m84047_230404_175159_s3.hifi_reads.unassigned.bam.pbi
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/m84047_230404_175159_s3.primary_qc.tar.xz b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/m84047_230404_175159_s3.primary_qc.tar.xz
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.scraps.bam.pbi
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.basecaller.log b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.basecaller.log
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.sts.xml
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.baz2bam.log b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.baz2bam.log
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam
diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.lima.log b/t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi
similarity index 100%
rename from t/data/pacbio/sequel/r84047_20230404_164149/1_C01/metadata/m84047_230404_175159_s3.fail_reads.lima.log
rename to t/data/pacbio/sequence/r54097_20170727_165601/1_A02/m54097_170727_170646.subreads.bam.pbi
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diff --git a/t/data/pacbio/sequel/r84098_20240219_101849/1_A01/fail_reads/m84098_240219_110741_s1.fail_reads.bc2076.bam b/t/data/pacbio/sequence/r64089e_20220615_171559/1_A01/m64089e_220615_173331.transferdone
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diff --git a/t/data/pacbio/sequel/r84098_20240219_101849/1_A01/hifi_reads/m84098_240219_110741_s1.hifi_reads.bc2076.bam b/t/data/pacbio/sequence/r64089e_20220930_164018/1_A01/bc1011_BAK8A_OA--bc1011_BAK8A_OA/m64089e_220930_165238.hifi_reads.bc1011_BAK8A_OA--bc1011_BAK8A_OA.bam
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old mode 100644
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old mode 100644
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old mode 100644
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diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.ccs_report.json b/t/data/pacbio/sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.ccs_report.json
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diff --git a/t/data/pacbio/sequel_analysis/0000020083/outputs/sample0.transcripts.cluster_report.csv b/t/data/pacbio/sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.lima_report.txt
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diff --git a/t/data/pacbio/sequel/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.unassigned.json b/t/data/pacbio/sequence/r84047_20230404_164149/1_C01/statistics/m84047_230404_175159_s3.fail_reads.unassigned.json
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diff --git a/t/data/pacbio/sequel_analysis/0000020156/outputs/transcripts.fasta b/t/data/pacbio/sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz
similarity index 100%
rename from t/data/pacbio/sequel_analysis/0000020156/outputs/transcripts.fasta
rename to t/data/pacbio/sequence/r84098_20240321_105751/1_A01/statistics/m84098_240321_114027_s1.zmw_metrics.json.gz
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitorTest.pm
similarity index 93%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitorTest.pm
index 5dac244d..8a82697f 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisMonitorTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisMonitorTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitorTest;
+package WTSI::NPG::HTS::PacBio::AnalysisMonitorTest;
 
 use strict;
 use warnings;
@@ -19,7 +19,7 @@ BEGIN {
 }
 
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor;
+use WTSI::NPG::HTS::PacBio::AnalysisMonitor;
 
 {
   package TestDB;
@@ -40,7 +40,7 @@ my $test_response =
     "name" => "TRAC-2-8046-Cell1_redo_demultiplex",
     "updatedAt" => "2024-04-08T16:39:32.434Z",
     "workflow" => "{}",
-    "path" => "t/data/pacbio/sequel_analysis/0000019480",
+    "path" => "t/data/pacbio/analysis/0000019480",
     "state" => "SUCCESSFUL",
     "tags" => "",
     "uuid" => "41b9c9b0-5621-41d8-a373-e04a641ddb2b",
@@ -118,7 +118,7 @@ sub publish_completed_jobs : Test(3) {
                                     strict_baton_version => 0);
   my $dest_coll = $irods_tmp_coll;
 
-  my $monitor = WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor->new
+  my $monitor = WTSI::NPG::HTS::PacBio::AnalysisMonitor->new
     (api_client         => $client,
      dest_collection    => $dest_coll,
      irods              => $irods,
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherTest.pm
similarity index 95%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherTest.pm
index adfaa365..76fdad53 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisPublisherTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisPublisherTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisherTest;
+package WTSI::NPG::HTS::PacBio::AnalysisPublisherTest;
 
 use strict;
 use warnings;
@@ -16,7 +16,7 @@ use Test::Exception;
 use base qw[WTSI::NPG::HTS::Test];
 use WTSI::NPG::HTS::LocationWriterTest;
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher;
+use WTSI::NPG::HTS::PacBio::AnalysisPublisher;
 use WTSI::NPG::iRODS;
 use WTSI::NPG::iRODS::DataObject;
 use WTSI::NPG::iRODS::Metadata;
@@ -32,8 +32,8 @@ Log::Log4perl::init('./etc/log4perl_tests.conf');
 
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel_analysis';
-my $rundata_path = 't/data/pacbio/sequel';
+my $data_path    = 't/data/pacbio/analysis';
+my $rundata_path = 't/data/pacbio/sequence';
 my $fixture_path = "t/fixtures";
 my $db_dir       = File::Temp->newdir;
 
@@ -69,7 +69,7 @@ sub teardown_test : Test(teardown) {
 }
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher');
+  require_ok('WTSI::NPG::HTS::PacBio::AnalysisPublisher');
 }
 
 sub script: Test(1) {
@@ -83,7 +83,7 @@ sub list_files : Test(3) {
   my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution",
   my $dest_coll      = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -122,7 +122,7 @@ sub publish_xml_files : Test(9) {
   my $dest_coll      = "$irods_tmp_coll/publish_xml_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -243,7 +243,7 @@ sub publish_sequence_files_4 : Test(4) {
   my $dest_coll      = "$irods_tmp_coll/publish_sequence_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -284,7 +284,7 @@ sub publish_files_4 : Test(6) {
   my $dest_coll      = "$irods_tmp_coll/publish_sequence_files";
   my $expected_json  = 't/data/mlwh_json/pacbio2.json';
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -338,7 +338,7 @@ sub publish_files_5 : Test(1) {
   my $runfolder_path = "$analysis_path/cromwell-job/call-lima/execution",
   my $dest_coll      = "$irods_tmp_coll/publish_sequence_files";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -360,7 +360,7 @@ sub list_files_2 : Test(2) {
   my $subdir_path    = "$analysis_path/bc1015_BAK8B_OA--bc1015_BAK8B_OA";  
   my $dest_coll      = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::AnalysisPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReportTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisReportTest.pm
similarity index 72%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReportTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/AnalysisReportTest.pm
index 6cce267c..fcfa07b8 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/AnalysisReportTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/AnalysisReportTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::AnalysisReportTest;
+package WTSI::NPG::HTS::PacBio::AnalysisReportTest;
 
 use strict;
 use warnings;
@@ -13,18 +13,18 @@ use Test::Exception;
 
 use base qw[WTSI::NPG::HTS::Test];
 
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::AnalysisReport;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 BEGIN {
   Log::Log4perl->init('./etc/log4perl_tests.conf');
 }
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel_analysis';
+my $data_path    = 't/data/pacbio/analysis';
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport');
+  require_ok('WTSI::NPG::HTS::PacBio::AnalysisReport');
 }
 
 sub read_report_file : Test(2) {
@@ -34,10 +34,10 @@ sub read_report_file : Test(2) {
   my $merged_file    = "$runfolder_path/merged_analysis_report.json";
 
   my $meta_file      = "$analysis_path/entry-points/2a711efd-0812-4a5f-b4a2-29714400611f.subreadset.xml";
-  my $meta_data      = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+  my $meta_data      = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
     ($meta_file, 'pbmeta:');
 
-  my $rdo = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->load($merged_file);
+  my $rdo = WTSI::NPG::HTS::PacBio::Reportdata->load($merged_file);
   
   cmp_ok($rdo->created_at, 'eq', '2021-05-10T11:23:36', 'created_at is correct');
   is_deeply($rdo->meta_data, $meta_data, 'meta_data is correct');
@@ -50,10 +50,10 @@ sub create_report_file_1 : Test(3) {
   my $report_file_1  = "$runfolder_path/merged_analysis_report.json";
 
   my $meta_file      = "$analysis_path/entry-points/7da072af-387d-49e8-8ee3-b0fa0c873fb7.subreadset.xml";
-  my $meta_data      = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+  my $meta_data      = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
     ($meta_file, 'pbmeta:');
 
-  my $rdo1 = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->load($report_file_1);
+  my $rdo1 = WTSI::NPG::HTS::PacBio::Reportdata->load($report_file_1);
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./report_tmp.XXXXXX");
   my @init_args = (
@@ -63,12 +63,12 @@ sub create_report_file_1 : Test(3) {
     meta_data      => $meta_data );
 
  
-  my $report = WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport->new(@init_args);
+  my $report = WTSI::NPG::HTS::PacBio::AnalysisReport->new(@init_args);
   my $report_file_name_2 = $report->generate_analysis_report;
   my $report_file_2 = catfile($report->output_dir,$report_file_name_2);
   ok(-f $report_file_2, "[2] created report file exists");
 
-  my $rdo2 = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->load($report_file_2);
+  my $rdo2 = WTSI::NPG::HTS::PacBio::Reportdata->load($report_file_2);
 
   is_deeply($rdo1->meta_data, $rdo2->meta_data, '[1] created report meta_data is correct');
   is_deeply($rdo1->reports, $rdo2->reports, '[1] created report reports is correct');
@@ -82,10 +82,10 @@ sub create_report_file_2 : Test(3) {
   my $report_file_1  = "$runfolder_path/merged_analysis_report.json";
 
   my $meta_file      = "$analysis_path/entry-points/081746ec-5099-4efb-9702-0f97bf22dc59.subreadset.xml";
-  my $meta_data      = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file
+  my $meta_data      = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file
     ($meta_file, 'pbmeta:');
 
-  my $rdo1 = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->load($report_file_1);
+  my $rdo1 = WTSI::NPG::HTS::PacBio::Reportdata->load($report_file_1);
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./report_tmp.XXXXXX");
   my @init_args = (
@@ -95,12 +95,12 @@ sub create_report_file_2 : Test(3) {
     meta_data      => $meta_data );
 
  
-  my $report = WTSI::NPG::HTS::PacBio::Sequel::AnalysisReport->new(@init_args);
+  my $report = WTSI::NPG::HTS::PacBio::AnalysisReport->new(@init_args);
   my $report_file_name_2 = $report->generate_analysis_report;
   my $report_file_2 = catfile($report->output_dir,$report_file_name_2);
   ok(-f $report_file_2, "[3] created report file exists");
 
-  my $rdo2 = WTSI::NPG::HTS::PacBio::Sequel::Reportdata->load($report_file_2);
+  my $rdo2 = WTSI::NPG::HTS::PacBio::Reportdata->load($report_file_2);
 
   is_deeply($rdo1->meta_data, $rdo2->meta_data, '[2] created report meta_data is correct');
   is_deeply($rdo1->reports, $rdo2->reports, '[2] created report reports is correct');
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchiveTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/ImageArchiveTest.pm
similarity index 79%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchiveTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/ImageArchiveTest.pm
index eb617f93..19597c57 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/ImageArchiveTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/ImageArchiveTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::ImageArchiveTest;
+package WTSI::NPG::HTS::PacBio::ImageArchiveTest;
 
 use strict;
 use warnings;
@@ -17,8 +17,8 @@ use base qw[WTSI::NPG::HTS::Test];
 
 use WTSI::DNAP::Utilities::Runnable;
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::ImageArchive;
-use WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser;
+use WTSI::NPG::HTS::PacBio::ImageArchive;
+use WTSI::NPG::HTS::PacBio::MetaXMLParser;
 
 BEGIN {
   Log::Log4perl->init('./etc/log4perl_tests.conf');
@@ -26,7 +26,7 @@ BEGIN {
 
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel_analysis';
+my $data_path    = 't/data/pacbio/analysis';
 
 my $user_agent;
 sub setup_useragent : Test(startup) {
@@ -43,7 +43,7 @@ sub setup_useragent : Test(startup) {
       modifiedAt=> '2020-12-28T16::36::56.212Z',
       name=> 'Adapter Report',
       fileTypeId=> 'PacBio.FileTypes.JsonReport',
-      path=> 't/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json',
+      path=> 't/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/adapter.report.json',
       description=> 'PacBio Report adapter_xml_report (7e21ed06-4cf8-45f1-ba5c-e5f20c8d11c4)',
       uuid=> '7e21ed06-4cf8-45f1-ba5c-e5f20c8d11c4',
       fileSize=> 835,
@@ -59,7 +59,7 @@ sub setup_useragent : Test(startup) {
       modifiedAt=> '2020-12-28T16::36::56.213Z',
       name=> 'Control Report',
       fileTypeId=> 'PacBio.FileTypes.JsonReport',
-      path=> 't/data/pacbio/sequel_analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json',
+      path=> 't/data/pacbio/analysis/0000003462/cromwell-job/call-sl_dataset_reports/sl_dataset_reports/75cf695b/call-import_dataset_reports/execution/control.report.json',
       description=> 'PacBio Report control (07dcba58-8da1-462a-b6ce-f5647a85af99)',
       uuid=> '07dcba58-8da1-462a-b6ce-f5647a85af99',
       fileSize=> 2166,
@@ -77,17 +77,17 @@ sub setup_useragent : Test(startup) {
 }
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::ImageArchive');
+  require_ok('WTSI::NPG::HTS::PacBio::ImageArchive');
 }
 
 sub create_image_archive : Test(2) {
 
   my $run_name  = 'r54097_20170727_165601';
   my $well      = '1_A02';
-  my $data_path = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path = catdir('t/data/pacbio/sequence', $run_name, $well);
 
   my $metafile  = catfile($data_path,'m54097_170727_170646.subreadset.xml');
-  my $metadata  = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file($metafile);
+  my $metadata  = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file($metafile);
 
   my $client    = WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(user_agent => $user_agent);
 
@@ -96,7 +96,7 @@ sub create_image_archive : Test(2) {
                    dataset_id   => $metadata->subreads_uuid,
                    output_dir   => tempdir(CLEANUP => 1));
 
-  my $ia = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@init_args);
+  my $ia = WTSI::NPG::HTS::PacBio::ImageArchive->new(@init_args);
   my $archive_file = $ia->generate_image_archive;
   ok(-f $archive_file, "created archive file exists");
 
@@ -111,10 +111,10 @@ sub create_image_archive_with_report_count : Test(2) {
 
   my $run_name   = 'r54097_20170727_165601';
   my $well       = '1_A02';
-  my $data_path  = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path  = catdir('t/data/pacbio/sequence', $run_name, $well);
 
   my $metafile   = catfile($data_path,'m54097_170727_170646.subreadset.xml');
-  my $metadata   = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file($metafile);
+  my $metadata   = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file($metafile);
 
   my $client    = WTSI::NPG::HTS::PacBio::Sequel::APIClient->new(user_agent => $user_agent);
 
@@ -127,7 +127,7 @@ sub create_image_archive_with_report_count : Test(2) {
   push @init_args1, report_count => '4';
   push @init_args1, output_dir   => tempdir(CLEANUP => 1);
 
-  my $ia1 = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@init_args1);
+  my $ia1 = WTSI::NPG::HTS::PacBio::ImageArchive->new(@init_args1);
   my $archive_file1 = $ia1->generate_image_archive;
   ok(! -f $archive_file1, "skipped creating archive file with incorrect qc file count");
 
@@ -136,7 +136,7 @@ sub create_image_archive_with_report_count : Test(2) {
   push @init_args2, report_count => '2';
   push @init_args2, output_dir   => tempdir(CLEANUP => 1);
 
-  my $ia2 = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@init_args2);
+  my $ia2 = WTSI::NPG::HTS::PacBio::ImageArchive->new(@init_args2);
   my $archive_file2 = $ia2->generate_image_archive;
   ok(-f $archive_file2, "created archive file with 2 report files exists");
 }
@@ -145,10 +145,10 @@ sub create_image_archive_with_specified_files : Test(2) {
 
   my $run_name  = 'r64174e_20210114_161659';
   my $well      = '1_A01';
-  my $data_path = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path = catdir('t/data/pacbio/sequence', $run_name, $well);
 
   my $metafile  = catfile($data_path,'m64174e_210114_162751.consensusreadset.xml');
-  my $metadata  = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file($metafile, q[pbmeta:]);
+  my $metadata  = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file($metafile, q[pbmeta:]);
 
   my @files     = (catfile($data_path,'m64174e_210114_162751.ccs_reports.json'));
 
@@ -162,7 +162,7 @@ sub create_image_archive_with_specified_files : Test(2) {
                    report_count    => '3',
                    specified_files => \@files);
 
-  my $ia = WTSI::NPG::HTS::PacBio::Sequel::ImageArchive->new(@init_args);
+  my $ia = WTSI::NPG::HTS::PacBio::ImageArchive->new(@init_args);
   my $archive_file = $ia->generate_image_archive;
   ok(-f $archive_file, "created archive file with specified file exists");
 
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisherTest.pm
similarity index 96%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisherTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisherTest.pm
index 15eecd3a..29f7968f 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/IsoSeqPublisherTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/IsoSeqPublisherTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisherTest;
+package WTSI::NPG::HTS::PacBio::IsoSeqPublisherTest;
 
 use strict;
 use warnings;
@@ -16,7 +16,7 @@ use Test::Exception;
 use base qw[WTSI::NPG::HTS::Test];
 use WTSI::NPG::HTS::LocationWriterTest;
 
-use WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher;
+use WTSI::NPG::HTS::PacBio::IsoSeqPublisher;
 
 use WTSI::NPG::iRODS;
 use WTSI::NPG::iRODS::DataObject;
@@ -33,8 +33,8 @@ Log::Log4perl::init('./etc/log4perl_tests.conf');
 
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel_analysis';
-my $rundata_path = 't/data/pacbio/sequel';
+my $data_path    = 't/data/pacbio/analysis';
+my $rundata_path = 't/data/pacbio/sequence';
 my $fixture_path = "t/fixtures";
 my $db_dir       = File::Temp->newdir;
 
@@ -69,7 +69,7 @@ sub teardown_test : Test(teardown) {
 }
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher');
+  require_ok('WTSI::NPG::HTS::PacBio::IsoSeqPublisher');
 }
 
 sub publish_files_1 : Test(5) {
@@ -82,7 +82,7 @@ sub publish_files_1 : Test(5) {
   my $dest_coll      = "$irods_tmp_coll/publish_sequence_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::IsoSeqPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -186,7 +186,7 @@ sub publish_files_2 : Test(5) {
   my $dest_coll      = "$irods_tmp_coll/publish_sequence_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::IsoSeqPublisher->new
     (restart_file    => catfile($tmpdir->dirname, 'published.json'),
      dest_collection => $dest_coll,
      irods           => $irods,
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditorTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/RunAuditorTest.pm
similarity index 93%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditorTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/RunAuditorTest.pm
index 473e8690..1bc96216 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunAuditorTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/RunAuditorTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunAuditorTest;
+package WTSI::NPG::HTS::PacBio::RunAuditorTest;
 
 use strict;
 use warnings;
@@ -21,9 +21,9 @@ BEGIN {
   Log::Log4perl->init('./etc/log4perl_tests.conf');
 }
 
-use WTSI::NPG::HTS::PacBio::Sequel::RunAuditor;
+use WTSI::NPG::HTS::PacBio::RunAuditor;
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
+use WTSI::NPG::HTS::PacBio::RunMonitor;
 use WTSI::NPG::iRODS;
 
 {
@@ -113,7 +113,7 @@ sub teardown_test : Test(teardown) {
 
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::RunAuditor');
+  require_ok('WTSI::NPG::HTS::PacBio::RunAuditor');
 }
 
 sub audit_runs : Test(26) {
@@ -128,7 +128,7 @@ sub audit_runs : Test(26) {
   my $run_name   = 'r54097_20170727_165601';
   my $well       = '1_A02';
 
-  my $data_path  = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path  = catdir('t/data/pacbio/sequence', $run_name, $well);
   my $dest_coll  = catdir($irods_tmp_coll, $run_name);
 
   my $runfolder_path = catdir($tmp_dir,$run_name);
@@ -152,7 +152,7 @@ sub audit_runs : Test(26) {
   my @n_init_args = (@init_args, check_format => 0, dry_run => 1);
   my @d_init_args = (@init_args, check_format => 0, dry_run => 0);
 
-  my $auditor1 = WTSI::NPG::HTS::PacBio::Sequel::RunAuditor->new(@c_init_args);
+  my $auditor1 = WTSI::NPG::HTS::PacBio::RunAuditor->new(@c_init_args);
 
   throws_ok { $auditor1->valid_runfolder_format($runfolder_path)} qr/Folder failed format checks/,
     'Expected runfolder path format error found';
@@ -177,7 +177,7 @@ sub audit_runs : Test(26) {
   cmp_ok($num_errors1, '==', 1, 'Expected error found [folder path format]');
 
   ## no folder format check, dry run
-  my $auditor2 = WTSI::NPG::HTS::PacBio::Sequel::RunAuditor->new(@n_init_args);
+  my $auditor2 = WTSI::NPG::HTS::PacBio::RunAuditor->new(@n_init_args);
   my ($num_run2, $num_processed2, $num_actioned2, $num_errors2) =
     $auditor2->check_runs;
 
@@ -188,7 +188,7 @@ sub audit_runs : Test(26) {
   cmp_ok($num_errors2, '==', 0, 'No errors found [folder path format]');
 
   ## no folder format check, no dry run, permissions default
-  my $auditor3 = WTSI::NPG::HTS::PacBio::Sequel::RunAuditor->new(@d_init_args);
+  my $auditor3 = WTSI::NPG::HTS::PacBio::RunAuditor->new(@d_init_args);
   my ($num_run3, $num_processed3, $num_actioned3, $num_errors3) =
     $auditor3->check_runs;
 
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitorTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitorTest.pm
similarity index 93%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitorTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitorTest.pm
index bad14c58..61b8d2d0 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteMonitorTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/RunDeleteMonitorTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitorTest;
+package WTSI::NPG::HTS::PacBio::RunDeleteMonitorTest;
 
 use strict;
 use warnings;
@@ -21,10 +21,10 @@ BEGIN {
   Log::Log4perl->init('./etc/log4perl_tests.conf');
 }
 
-use WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor;
+use WTSI::NPG::HTS::PacBio::RunDeleteMonitor;
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
+use WTSI::NPG::HTS::PacBio::RunMonitor;
+use WTSI::NPG::HTS::PacBio::RunPublisher;
 use WTSI::NPG::DriRODS;
 use WTSI::NPG::iRODS;
 
@@ -185,7 +185,7 @@ sub teardown_test : Test(teardown) {
 
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor');
+  require_ok('WTSI::NPG::HTS::PacBio::RunDeleteMonitor');
 }
 
 sub script: Test(1) {
@@ -206,7 +206,7 @@ sub delete_runs : Test(14) {
   my $run_name   = 'r54097_20170727_165601';
   my $well       = '1_A02';
 
-  my $data_path  = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path  = catdir('t/data/pacbio/sequence', $run_name, $well);
   my $dest_coll  = catdir($irods_tmp_coll, $run_name);
 
   my $runfolder_path = catdir($tmp_dir,$run_name);
@@ -217,7 +217,7 @@ sub delete_runs : Test(14) {
   chmod (0770, $runfolder_data) or die "Chmod 0770 directory $runfolder_data failed : $!";
 
   ## publish data
-  my $monitor = WTSI::NPG::HTS::PacBio::Sequel::RunMonitor->new
+  my $monitor = WTSI::NPG::HTS::PacBio::RunMonitor->new
     (api_client         => $client,
      dest_collection    => $dest_coll,
      irods              => $irods,
@@ -232,7 +232,7 @@ sub delete_runs : Test(14) {
   cmp_ok($num_errors, '==', 0, 'No error in any run published');
 
   ## delete run successfully
-  my $deletable = WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor->new
+  my $deletable = WTSI::NPG::HTS::PacBio::RunDeleteMonitor->new
     (api_client         => $client,
      check_format       => 0,
      dest_collection    => $dest_coll,
@@ -292,7 +292,7 @@ sub delete_run_on_board_deplexing : Test(7) {
   my $run_name   = 'r64089e_20220615_171559';
   my $well       = '1_A01';
 
-  my $data_path  = catdir('t/data/pacbio/sequel', $run_name, $well);
+  my $data_path  = catdir('t/data/pacbio/sequence', $run_name, $well);
   my $dest_coll  = catdir($irods_tmp_coll, $run_name);
 
   my $runfolder_path = catdir($tmp_dir,$run_name);
@@ -303,7 +303,7 @@ sub delete_run_on_board_deplexing : Test(7) {
   chmod (0770, $runfolder_data) or die "Chmod 0770 directory $runfolder_data failed : $!";
 
   ## publish data
-  my $monitor = WTSI::NPG::HTS::PacBio::Sequel::RunMonitor->new
+  my $monitor = WTSI::NPG::HTS::PacBio::RunMonitor->new
     (api_client         => $client,
      dest_collection    => $dest_coll,
      irods              => $irods,
@@ -318,7 +318,7 @@ sub delete_run_on_board_deplexing : Test(7) {
   cmp_ok($num_errors, '==', 0, 'No error in any run published');
 
   ## delete run successfully
-  my $deletable = WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor->new
+  my $deletable = WTSI::NPG::HTS::PacBio::RunDeleteMonitor->new
     (api_client         => $client,
      check_format       => 0,
      dest_collection    => $dest_coll,
@@ -350,7 +350,7 @@ sub delete_run_on_board_deplexing_fail : Test(6) {
 
   ## create tmp runfolder which will be deleted later
   my $run_name   = 'r64089e_20220930_164018';
-  my $data_path  = catdir('t/data/pacbio/sequel', $run_name);
+  my $data_path  = catdir('t/data/pacbio/sequence', $run_name);
 
   my $dest_coll  = catdir($irods_tmp_coll, $run_name);
   my $runfolder_path = catdir($tmp_dir,$run_name);
@@ -360,7 +360,7 @@ sub delete_run_on_board_deplexing_fail : Test(6) {
   chmod (0770, "$runfolder_path/1_A01") or die "Chmod 0770 directory failed : $!";  
   chmod (0770, "$runfolder_path/2_B01") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -373,7 +373,7 @@ sub delete_run_on_board_deplexing_fail : Test(6) {
   cmp_ok($num_errors,    '==', 1, 'One error in one run published');
 
   ## attempt to delete run
-  my $deletable = WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor->new
+  my $deletable = WTSI::NPG::HTS::PacBio::RunDeleteMonitor->new
     (api_client         => $client,
      check_format       => 0,
      dest_collection    => $dest_coll,
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/RunDeleteTest.pm
similarity index 68%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/RunDeleteTest.pm
index 64d044b2..9715c9a4 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunDeleteTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/RunDeleteTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunDeleteTest;
+package WTSI::NPG::HTS::PacBio::RunDeleteTest;
 
 use strict;
 use warnings;
@@ -15,15 +15,15 @@ BEGIN {
   Log::Log4perl->init('./etc/log4perl_tests.conf');
 }
 
-use WTSI::NPG::HTS::PacBio::Sequel::RunDelete;
+use WTSI::NPG::HTS::PacBio::RunDelete;
 
 my $pid           = $PID;
 my $test_counter  = 0;
-my $data_path     = 't/data/pacbio/sequel';
+my $data_path     = 't/data/pacbio/sequence';
 my $tmp_dir       = File::Temp->newdir;
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::RunDelete');
+  require_ok('WTSI::NPG::HTS::PacBio::RunDelete');
 }
 
 sub delete_run : Test(4) {
@@ -31,10 +31,10 @@ sub delete_run : Test(4) {
    my $tmp_output_dir     = "$tmp_dir/rundeletefolder.$pid";
    make_path($tmp_output_dir);
 
-   my $deleter = WTSI::NPG::HTS::PacBio::Sequel::RunDelete->new
+   my $deleter = WTSI::NPG::HTS::PacBio::RunDelete->new
        (runfolder_path => $tmp_output_dir);
 
-   isa_ok($deleter, 'WTSI::NPG::HTS::PacBio::Sequel::RunDelete');  
+   isa_ok($deleter, 'WTSI::NPG::HTS::PacBio::RunDelete');  
    ok(-d $tmp_output_dir, "Runfolder to be deleted exists");
    ok($deleter->delete_run(), "Deleted the runfolder directory");
    ok(! -d $tmp_output_dir, "Deleted runfolder doesn't exist");
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitorTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/RunMonitorTest.pm
similarity index 94%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitorTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/RunMonitorTest.pm
index fa29dc0a..be965afb 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunMonitorTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/RunMonitorTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunMonitorTest;
+package WTSI::NPG::HTS::PacBio::RunMonitorTest;
 
 use strict;
 use warnings;
@@ -20,7 +20,7 @@ BEGIN {
 }
 
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
+use WTSI::NPG::HTS::PacBio::RunMonitor;
 
 {
   package TestDB;
@@ -39,7 +39,7 @@ use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
 
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel';
+my $data_path    = 't/data/pacbio/sequence';
 my $fixture_path = "t/fixtures";
 my $db_dir       = File::Temp->newdir;
 
@@ -124,7 +124,7 @@ sub publish_completed_runs : Test(3) {
                                     strict_baton_version => 0);
   my $dest_coll = $irods_tmp_coll;
 
-  my $monitor = WTSI::NPG::HTS::PacBio::Sequel::RunMonitor->new
+  my $monitor = WTSI::NPG::HTS::PacBio::RunMonitor->new
     (api_client         => $client,
      dest_collection    => $dest_coll,
      irods              => $irods,
@@ -149,7 +149,7 @@ sub publish_completed_runs_none : Test(3) {
                                     strict_baton_version => 0);
   my $dest_coll = $irods_tmp_coll;
 
-  my $monitor = WTSI::NPG::HTS::PacBio::Sequel::RunMonitor->new
+  my $monitor = WTSI::NPG::HTS::PacBio::RunMonitor->new
     (api_client         => $client,
      dest_collection    => $dest_coll,
      irods              => $irods,
diff --git a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm b/t/lib/WTSI/NPG/HTS/PacBio/RunPublisherTest.pm
similarity index 94%
rename from t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm
rename to t/lib/WTSI/NPG/HTS/PacBio/RunPublisherTest.pm
index 487a65d0..cec69277 100644
--- a/t/lib/WTSI/NPG/HTS/PacBio/Sequel/RunPublisherTest.pm
+++ b/t/lib/WTSI/NPG/HTS/PacBio/RunPublisherTest.pm
@@ -1,4 +1,4 @@
-package WTSI::NPG::HTS::PacBio::Sequel::RunPublisherTest;
+package WTSI::NPG::HTS::PacBio::RunPublisherTest;
 
 use strict;
 use warnings;
@@ -15,8 +15,8 @@ use Test::More;
 use base qw[WTSI::NPG::HTS::Test];
 
 use WTSI::NPG::HTS::PacBio::Sequel::APIClient;
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
-use WTSI::NPG::HTS::PacBio::Sequel::Product;
+use WTSI::NPG::HTS::PacBio::RunPublisher;
+use WTSI::NPG::HTS::PacBio::Product;
 use WTSI::NPG::iRODS;
 use WTSI::NPG::iRODS::DataObject;
 use WTSI::NPG::iRODS::Metadata;
@@ -40,15 +40,15 @@ Log::Log4perl::init('./etc/log4perl_tests.conf');
 
 my $pid          = $PID;
 my $test_counter = 0;
-my $data_path    = 't/data/pacbio/sequel';
+my $data_path    = 't/data/pacbio/sequence';
 my $fixture_path = "t/fixtures";
 my $db_dir       = File::Temp->newdir;
 
-my $SEQUENCE_PRODUCT      = $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::SEQUENCE_PRODUCT;
-my $SEQUENCE_AUXILIARY    = $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::SEQUENCE_AUXILIARY;
-my $FILE_PREFIX_PATTERN   = $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::FILE_PREFIX_PATTERN;
-my $SEQUENCE_FILE_FORMAT  = $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::SEQUENCE_FILE_FORMAT;
-my $SEQUENCE_INDEX_FORMAT = $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::SEQUENCE_INDEX_FORMAT;
+my $SEQUENCE_PRODUCT      = $WTSI::NPG::HTS::PacBio::RunPublisher::SEQUENCE_PRODUCT;
+my $SEQUENCE_AUXILIARY    = $WTSI::NPG::HTS::PacBio::RunPublisher::SEQUENCE_AUXILIARY;
+my $FILE_PREFIX_PATTERN   = $WTSI::NPG::HTS::PacBio::RunPublisher::FILE_PREFIX_PATTERN;
+my $SEQUENCE_FILE_FORMAT  = $WTSI::NPG::HTS::PacBio::RunPublisher::SEQUENCE_FILE_FORMAT;
+my $SEQUENCE_INDEX_FORMAT = $WTSI::NPG::HTS::PacBio::RunPublisher::SEQUENCE_INDEX_FORMAT;
 
 my $wh_schema;
 
@@ -82,7 +82,7 @@ sub teardown_test : Test(teardown) {
 }
 
 sub require : Test(1) {
-  require_ok('WTSI::NPG::HTS::PacBio::Sequel::RunPublisher');
+  require_ok('WTSI::NPG::HTS::PacBio::RunPublisher');
 }
 
 sub script: Test(1) {
@@ -95,7 +95,7 @@ sub list_xml_files : Test(1) {
   my $runfolder_path = "$data_path/r54097_20170727_165601";
   my $dest_coll = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -116,7 +116,7 @@ sub list_aux_files : Test(1) {
   my $runfolder_path = "$data_path/r54097_20170727_165601";
   my $dest_coll = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -137,7 +137,7 @@ sub list_sequence_files : Test(2) {
   my $runfolder_path = "$data_path/r54097_20170727_165601";
   my $dest_coll = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -165,7 +165,7 @@ sub list_index_files : Test(1) {
   my $runfolder_path = "$data_path/r54097_20170727_165601";
   my $dest_coll = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -190,7 +190,7 @@ sub list_image_archive_files : Test(1) {
   my $runfolder_path = "$data_path/r54097_20170727_165601";
   my $dest_coll = $irods_tmp_coll;
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -217,7 +217,7 @@ sub publish_files_on_instrument_1 : Test(43) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -267,7 +267,7 @@ sub publish_files_on_instrument_2 : Test(86) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";
   
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -323,7 +323,7 @@ sub publish_files_on_instrument_3 : Test(3) {
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";  
   chmod (0770, "$tmprf_path/2_B01") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -385,7 +385,7 @@ sub publish_files_on_instrument_4 : Test(3) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";  
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -433,7 +433,7 @@ sub publish_files_on_instrument_5 : Test(184) {
   chmod (0770, "$tmprf_path/1_C01") or die "Chmod 0770 directory failed : $!";  
 
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -538,7 +538,7 @@ sub publish_files_on_instrument_6 : Test(79) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -601,7 +601,7 @@ sub publish_files_on_instrument_7 : Test(4) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A01") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -650,7 +650,7 @@ sub publish_files_off_instrument : Test(3) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A02") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -697,7 +697,7 @@ sub publish_only_runfolder_writable : Test(6) {
   chmod (0700, $tdata_path) or die "Chmod directory $tdata_path failed : $!";
 
   my $dest_coll = "$irods_tmp_coll/publish_runfolder_writable";
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -731,7 +731,7 @@ sub publish_xml_files : Test(14) {
   dircopy($runfolder_path,$tmprf_path) or die $!;
   chmod (0770, "$tmprf_path/1_A02") or die "Chmod 0770 directory failed : $!";
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -766,7 +766,7 @@ sub publish_aux_files : Test(9) {
   my $dest_coll = "$irods_tmp_coll/publish_adapter_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -800,7 +800,7 @@ sub publish_sequence_files : Test(42) {
   my $dest_coll = "$irods_tmp_coll/publish_sequence_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -809,7 +809,7 @@ sub publish_sequence_files : Test(42) {
 
   my $pattern  = $FILE_PREFIX_PATTERN .'[.]'. q[subreadset] .'[.]xml$';
   my $metafile = $pub->list_files('1_A02', $pattern, '1')->[0];
-  my $meta = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file($metafile);
+  my $meta = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file($metafile);
 
   my @expected_paths =
     map { catfile("$dest_coll/1_A02", $_) }
@@ -844,7 +844,7 @@ sub publish_index_files : Test(14) {
   my $dest_coll = "$irods_tmp_coll/publish_sequence_files";
 
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (dest_collection => $dest_coll,
      irods           => $irods,
      mlwh_schema     => $wh_schema,
@@ -882,7 +882,7 @@ sub publish_image_archive : Test(9) {
   my $client = TestAPIClient->new(default_interval => 10000,);
   my $tmpdir = File::Temp->newdir(TEMPLATE => "./batch_tmp.XXXXXX");
 
-  my $pub = WTSI::NPG::HTS::PacBio::Sequel::RunPublisher->new
+  my $pub = WTSI::NPG::HTS::PacBio::RunPublisher->new
     (api_client      => $client,
      dest_collection => $dest_coll,
      irods           => $irods,
@@ -892,7 +892,7 @@ sub publish_image_archive : Test(9) {
 
   my $pattern  = $FILE_PREFIX_PATTERN .'[.]'. q[subreadset] .'[.]xml$';
   my $metafile = $pub->list_files('1_A02', $pattern, '1')->[0];
-  my $meta = WTSI::NPG::HTS::PacBio::Sequel::MetaXMLParser->new->parse_file($metafile);
+  my $meta = WTSI::NPG::HTS::PacBio::MetaXMLParser->new->parse_file($metafile);
 
   my @expected_paths =
     map { catfile("$dest_coll/1_A02", $_) }
@@ -900,7 +900,7 @@ sub publish_image_archive : Test(9) {
 
   my ($num_files, $num_processed, $num_errors) =
     $pub->publish_image_archive('1_A02', $meta,
-    $WTSI::NPG::HTS::PacBio::Sequel::RunPublisher::OFFINSTRUMENT);
+    $WTSI::NPG::HTS::PacBio::RunPublisher::OFFINSTRUMENT);
 
   cmp_ok($num_files,     '==', scalar @expected_paths);
   cmp_ok($num_processed, '==', scalar @expected_paths);
@@ -981,7 +981,7 @@ sub check_primary_metadata {
     my @product_ids  = $obj->find_in_metadata($ID_PRODUCT);
     my $product_id = $product_ids[0]->{value};
 
-    my $product = WTSI::NPG::HTS::PacBio::Sequel::Product->new();
+    my $product = WTSI::NPG::HTS::PacBio::Product->new();
     my $expected_id;
     if ($obj->find_in_metadata($TARGET)){
       my @tag_meta = $obj->find_in_metadata($TAG_SEQUENCE);
diff --git a/t/pacbio_analysis_monitor.t b/t/pacbio_analysis_monitor.t
new file mode 100644
index 00000000..7a98892c
--- /dev/null
+++ b/t/pacbio_analysis_monitor.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::AnalysisMonitorTest;
+
+WTSI::NPG::HTS::PacBio::AnalysisMonitorTest->runtests;
diff --git a/t/pacbio_analysis_publisher.t b/t/pacbio_analysis_publisher.t
new file mode 100644
index 00000000..ec4b4c12
--- /dev/null
+++ b/t/pacbio_analysis_publisher.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::AnalysisPublisherTest;
+
+WTSI::NPG::HTS::PacBio::AnalysisPublisherTest->runtests;
diff --git a/t/pacbio_analysis_report.t b/t/pacbio_analysis_report.t
new file mode 100644
index 00000000..e319e1db
--- /dev/null
+++ b/t/pacbio_analysis_report.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::AnalysisReportTest;
+
+WTSI::NPG::HTS::PacBio::AnalysisReportTest->runtests;
diff --git a/t/pacbio_image_archive.t b/t/pacbio_image_archive.t
new file mode 100644
index 00000000..5719e913
--- /dev/null
+++ b/t/pacbio_image_archive.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::ImageArchiveTest;
+
+WTSI::NPG::HTS::PacBio::ImageArchiveTest->runtests;
diff --git a/t/pacbio_isoseq_publisher.t b/t/pacbio_isoseq_publisher.t
new file mode 100644
index 00000000..d4083d08
--- /dev/null
+++ b/t/pacbio_isoseq_publisher.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::IsoSeqPublisherTest;
+
+WTSI::NPG::HTS::PacBio::IsoSeqPublisherTest->runtests;
diff --git a/t/pacbio_run_auditor.t b/t/pacbio_run_auditor.t
new file mode 100644
index 00000000..637101fc
--- /dev/null
+++ b/t/pacbio_run_auditor.t
@@ -0,0 +1,6 @@
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::RunAuditorTest;
+
+WTSI::NPG::HTS::PacBio::RunAuditorTest->runtests;
diff --git a/t/pacbio_run_delete.t b/t/pacbio_run_delete.t
new file mode 100644
index 00000000..fbfd7129
--- /dev/null
+++ b/t/pacbio_run_delete.t
@@ -0,0 +1,6 @@
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::RunDeleteTest;
+
+WTSI::NPG::HTS::PacBio::RunDeleteTest->runtests;
diff --git a/t/pacbio_run_delete_monitor.t b/t/pacbio_run_delete_monitor.t
new file mode 100644
index 00000000..a879629e
--- /dev/null
+++ b/t/pacbio_run_delete_monitor.t
@@ -0,0 +1,6 @@
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::RunDeleteMonitorTest;
+
+WTSI::NPG::HTS::PacBio::RunDeleteMonitorTest->runtests;
diff --git a/t/pacbio_run_monitor.t b/t/pacbio_run_monitor.t
new file mode 100644
index 00000000..0ffda2d7
--- /dev/null
+++ b/t/pacbio_run_monitor.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::RunMonitorTest;
+
+WTSI::NPG::HTS::PacBio::RunMonitorTest->runtests;
diff --git a/t/pacbio_run_publisher.t b/t/pacbio_run_publisher.t
new file mode 100644
index 00000000..911f738c
--- /dev/null
+++ b/t/pacbio_run_publisher.t
@@ -0,0 +1,7 @@
+
+use strict;
+use warnings;
+
+use WTSI::NPG::HTS::PacBio::RunPublisherTest;
+
+WTSI::NPG::HTS::PacBio::RunPublisherTest->runtests;
diff --git a/t/pacbio_sequel_analysis_monitor.t b/t/pacbio_sequel_analysis_monitor.t
deleted file mode 100644
index a9ce604f..00000000
--- a/t/pacbio_sequel_analysis_monitor.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitorTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitorTest->runtests;
diff --git a/t/pacbio_sequel_analysis_publisher.t b/t/pacbio_sequel_analysis_publisher.t
deleted file mode 100644
index 51b1ca64..00000000
--- a/t/pacbio_sequel_analysis_publisher.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisherTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisPublisherTest->runtests;
diff --git a/t/pacbio_sequel_analysis_report.t b/t/pacbio_sequel_analysis_report.t
deleted file mode 100644
index e27ebc59..00000000
--- a/t/pacbio_sequel_analysis_report.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisReportTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::AnalysisReportTest->runtests;
diff --git a/t/pacbio_sequel_image_archive.t b/t/pacbio_sequel_image_archive.t
deleted file mode 100644
index 4792a049..00000000
--- a/t/pacbio_sequel_image_archive.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::ImageArchiveTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::ImageArchiveTest->runtests;
diff --git a/t/pacbio_sequel_isoseq_publisher.t b/t/pacbio_sequel_isoseq_publisher.t
deleted file mode 100644
index aa624cfa..00000000
--- a/t/pacbio_sequel_isoseq_publisher.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisherTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::IsoSeqPublisherTest->runtests;
diff --git a/t/pacbio_sequel_run_auditor.t b/t/pacbio_sequel_run_auditor.t
deleted file mode 100644
index 19c87a40..00000000
--- a/t/pacbio_sequel_run_auditor.t
+++ /dev/null
@@ -1,6 +0,0 @@
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::RunAuditorTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::RunAuditorTest->runtests;
diff --git a/t/pacbio_sequel_run_delete.t b/t/pacbio_sequel_run_delete.t
deleted file mode 100644
index 3dd3e39c..00000000
--- a/t/pacbio_sequel_run_delete.t
+++ /dev/null
@@ -1,6 +0,0 @@
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::RunDeleteTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::RunDeleteTest->runtests;
diff --git a/t/pacbio_sequel_run_delete_monitor.t b/t/pacbio_sequel_run_delete_monitor.t
deleted file mode 100644
index f134f8f8..00000000
--- a/t/pacbio_sequel_run_delete_monitor.t
+++ /dev/null
@@ -1,6 +0,0 @@
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitorTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitorTest->runtests;
diff --git a/t/pacbio_sequel_run_monitor.t b/t/pacbio_sequel_run_monitor.t
deleted file mode 100644
index f74b4a0b..00000000
--- a/t/pacbio_sequel_run_monitor.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitorTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::RunMonitorTest->runtests;
diff --git a/t/pacbio_sequel_run_publisher.t b/t/pacbio_sequel_run_publisher.t
deleted file mode 100644
index e5be1cf7..00000000
--- a/t/pacbio_sequel_run_publisher.t
+++ /dev/null
@@ -1,7 +0,0 @@
-
-use strict;
-use warnings;
-
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisherTest;
-
-WTSI::NPG::HTS::PacBio::Sequel::RunPublisherTest->runtests;

From 188688648dcebe536f916640fb65b07471577aea Mon Sep 17 00:00:00 2001
From: Keith James <kdj@sanger.ac.uk>
Date: Wed, 11 Sep 2024 16:00:25 +0100
Subject: [PATCH 2/3] Update Perlbrew checksum for release 0.99

---
 .github/workflows/perlbrew.sha256 | 2 +-
 Changes                           | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/perlbrew.sha256 b/.github/workflows/perlbrew.sha256
index d9992912..b075ba80 100644
--- a/.github/workflows/perlbrew.sha256
+++ b/.github/workflows/perlbrew.sha256
@@ -1 +1 @@
-c3996e4fae37a0ae01839cdd73752fb7b17e81bac2a8b39712463a7d518c4945  perlbrew.sh
+8f254651d2eee188199b3355228eb67166974716081b794ca93b69c8f949c38d perlbrew.sh
diff --git a/Changes b/Changes
index 5e15ca9a..4cb56ca7 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,13 @@
 Unreleased
 
+ - Following a release on 07/09/2024, see https://metacpan.org/dist/App-perlbrew/changes
+   the checksum of the script served by https://install.perlbrew.pl had changed.
+   https://install.perlbrew.pl is a redirect to raw
+   https://github.com/gugod/App-perlbrew/blob/master/perlbrew-install, so
+   the change originates from GitHub and can be trusted. Our CI flow compares
+   the checksum of the downloaded script to the expected value. We now store
+   an updated expected checksum value, which corresponds to the latest release.
+
 Release 2.50.0 (2024-08-07)
  - SMRT Link IsoSeq analysis has changed substantially in SMRT Link v13
    so old code and tests related to this was removed - further work is

From 3fc82e8c294df5f1059aef280c3da0ef98348fb0 Mon Sep 17 00:00:00 2001
From: Carol Scott <ces@sanger.ac.uk>
Date: Wed, 18 Sep 2024 14:11:40 +0100
Subject: [PATCH 3/3] Fix scripts

---
 bin/npg_pacbio_analysis_monitor.pl | 2 +-
 bin/npg_pacbio_run_auxiliary.pl    | 4 ++--
 bin/npg_pacbio_runmonitor.pl       | 2 +-
 bin/npg_publish_pacbio_run.pl      | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/bin/npg_pacbio_analysis_monitor.pl b/bin/npg_pacbio_analysis_monitor.pl
index 5de04fa0..23929801 100755
--- a/bin/npg_pacbio_analysis_monitor.pl
+++ b/bin/npg_pacbio_analysis_monitor.pl
@@ -13,7 +13,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::AnalysisMonitor;
+use WTSI::NPG::HTS::PacBio::AnalysisMonitor;
 
 our $VERSION = '';
 
diff --git a/bin/npg_pacbio_run_auxiliary.pl b/bin/npg_pacbio_run_auxiliary.pl
index 63e8255d..c8d00e62 100755
--- a/bin/npg_pacbio_run_auxiliary.pl
+++ b/bin/npg_pacbio_run_auxiliary.pl
@@ -13,8 +13,8 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::DriRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunDeleteMonitor;
-use WTSI::NPG::HTS::PacBio::Sequel::RunAuditor;
+use WTSI::NPG::HTS::PacBio::RunDeleteMonitor;
+use WTSI::NPG::HTS::PacBio::RunAuditor;
 
 our $VERSION = '';
 
diff --git a/bin/npg_pacbio_runmonitor.pl b/bin/npg_pacbio_runmonitor.pl
index 86ccc14e..5c6cdad9 100755
--- a/bin/npg_pacbio_runmonitor.pl
+++ b/bin/npg_pacbio_runmonitor.pl
@@ -13,7 +13,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunMonitor;
+use WTSI::NPG::HTS::PacBio::RunMonitor;
 
 
 our $VERSION = '';
diff --git a/bin/npg_publish_pacbio_run.pl b/bin/npg_publish_pacbio_run.pl
index 7a44b7ca..7b5bfbc4 100755
--- a/bin/npg_publish_pacbio_run.pl
+++ b/bin/npg_publish_pacbio_run.pl
@@ -11,7 +11,7 @@
 
 use WTSI::DNAP::Warehouse::Schema;
 use WTSI::NPG::iRODS;
-use WTSI::NPG::HTS::PacBio::Sequel::RunPublisher;
+use WTSI::NPG::HTS::PacBio::RunPublisher;
 
 our $VERSION = '';