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MANIFEST
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bin/create_summary_link
bin/npg_pipeline_archival_runner
bin/npg_pipeline_central
bin/npg_pipeline_check_bam_file_cluster_count
bin/npg_pipeline_analysis_runner
bin/npg_pipeline_job_env_to_threads
bin/npg_pipeline_post_qc_review
bin/npg_pipeline_preexec_references
bin/npg_pipeline_seqchksum_comparator
bin/script_must_be_unique_runner
Build.PL
Changes
data/config_files/function_list_central.yml
data/config_files/function_list_central_gclp.yml
data/config_files/function_list_central_olb.yml
data/config_files/function_list_central_qc_run.yml
data/config_files/function_list_post_qc_review.yml
data/config_files/function_list_post_qc_review_gclp.yml
data/config_files/general_values.ini
data/config_files/illumina_pipeline.ini
data/config_files/parallelisation.yml
data/config_files/pb_cal_pipeline.ini
lib/npg_pipeline/analysis/bustard4pbcb.pm
lib/npg_pipeline/analysis/create_lane_tag_file.pm
lib/npg_pipeline/analysis/FixConfigFiles.pm
lib/npg_pipeline/analysis/harold_calibration_bam.pm
lib/npg_pipeline/analysis/split_bam_by_tag.pm
lib/npg_pipeline/archive/file/BamClusterCounts.pm
lib/npg_pipeline/archive/file/generation.pm
lib/npg_pipeline/archive/file/generation/illumina2bam.pm
lib/npg_pipeline/archive/file/generation/seq_alignment.pm
lib/npg_pipeline/archive/file/qc.pm
lib/npg_pipeline/archive/file/generation/seqchksum_comparator.pm
lib/npg_pipeline/archive/file/to_irods.pm
lib/npg_pipeline/archive/file/logs.pm
lib/npg_pipeline/archive/folder/generation.pm
lib/npg_pipeline/archive/qc/auto_qc.pm
lib/npg_pipeline/archive/qc/fastqcheck_loader.pm
lib/npg_pipeline/archive/qc/illumina_analysis.pm
lib/npg_pipeline/base.pm
lib/npg_pipeline/cache.pm
lib/npg_pipeline/daemon/archival.pm
lib/npg_pipeline/daemon/analysis.pm
lib/npg_pipeline/daemon.pm
lib/npg_pipeline/dispatch_tree.pm
lib/npg_pipeline/launcher/status.pm
lib/npg_pipeline/lsf_job.pm
lib/npg_pipeline/pluggable.pm
lib/npg_pipeline/pluggable/harold.pm
lib/npg_pipeline/pluggable/harold/central.pm
lib/npg_pipeline/pluggable/harold/post_qc_review.pm
lib/npg_pipeline/roles/accessor.pm
lib/npg_pipeline/roles/business/base.pm
lib/npg_pipeline/roles/business/flag_options.pm
lib/npg_pipeline/roles/business/harold_calibration_reqs.pm
lib/npg_pipeline/run/folder/link.pm
lib/npg_tracking/daemon/analysis.pm
lib/npg_tracking/daemon/archival.pm
MANIFEST This list of files
README
t/00-critic.t
t/00-distribution.t
t/00-pod.t
t/00-podcoverage.t
t/00-scripts-compile.t
t/10-base.t
t/10-cache.t
t/10-lsf_job.t
t/10-pluggable.t
t/10-pluggable_harold.t
t/10-pluggable_harold_central.t
t/10-pluggable_harold_post_qc_review.t
t/10-script-job_env_to_threads.t
t/15-pipeline_launcher_scripts.t
t/20-archive-fastqcheck.t
t/20-archive_auto_qc_to_db.t
t/20-archive_file-to_irods.t
t/20-archive_file_generation-illumina2bam.t
t/20-archive_file_generation-seq_alignment.t
t/20-archive_folder_generation.t
t/20-archive_illumina_analysis.t
t/20-archive_qc.t
t/20-archive_logs.t
t/21-references_adapters.t
t/25-analysis-bustard4pbcb.t
t/25-analysis-create_lane_tag_file.t
t/25-analysis-FixConfigFiles.t
t/25-analysis-split_bam_by_tag.t
t/25-harold_calibration_bam.t
t/30-launcher-status.t
t/30-run_folder-link.t
t/35-archive_file_generation-BamClusterCounts.t
t/35-archive-file-generation-seqchksum_comparator.t
t/40-dispatch_tree.t
t/50-npg_pipeline-daemon-archival.t
t/50-npg_pipeline-daemon-analysis.t
t/60-npg_tracking-daemon-analysis.t
t/60-npg_tracking-daemon-archival.t
t/bin/bkill
t/bin/bresume
t/bin/bsub
t/bin/dodo/lsadmin
t/bin/dodo/machine-location
t/bin/lenny/lsadmin
t/bin/lsadmin
t/bin/machine-location
t/bin/red/machine-location
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/AlignmentFilter.jar
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/BamAdapterFinder.jar
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/BamIndexDecoder.jar
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/BamMerger.jar
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/Illumina2bam.jar
t/bin/software/solexa/bin/aligners/illumina2bam/Illumina2bam-tools-1.00/SplitBamByReadGroup.jar
t/bin/software/solexa/bin/qc
t/data/samplesheet_1234.csv
t/data/illumina2bam/1234_samplesheet.csv
t/data/qc/1234_samplesheet_amended.csv
t/data/qc/samplesheet_14353.csv
t/data/qc/samplesheet_14043.csv
t/data/qc/references/PhiX/default/all/fasta/PhiX.fasta
t/data/qc/references/Homo_sapiens/1000Genomes_hs37d5/all/fasta/hs37d5.fa
t/data/bam_flagstats/1234_1_bam_flagstats.json
t/data/bam_flagstats/1234_3_bam_flagstats.json
t/data/bam_flagstats/1234_3_phix_bam_flagstats.json
t/data/bam_flagstats/1234_4_bam_flagstats.json
t/data/cache/xml/npg/instrument/103.xml
t/data/cache/xml/npg/run/12376.xml
t/data/cache/xml/npg/run_status_dict.xml
t/data/cache/my_samplesheet_12376.csv
t/data/dbic_fixtures/000-Designation.yml
t/data/dbic_fixtures/000-EntityType.yml
t/data/dbic_fixtures/000-InstrumentStatusDict.yml
t/data/dbic_fixtures/000-RunLaneStatusDict.yml
t/data/dbic_fixtures/000-RunStatusDict.yml
t/data/dbic_fixtures/000-Tag.yml
t/data/dbic_fixtures/000-User.yml
t/data/dbic_fixtures/000-Usergroup.yml
t/data/dbic_fixtures/100-EventType.yml
t/data/dbic_fixtures/100-InstrumentFormat.yml
t/data/dbic_fixtures/100-User2usergroup.yml
t/data/dbic_fixtures/200-Event.yml
t/data/dbic_fixtures/200-Instrument.yml
t/data/dbic_fixtures/300-Run.yml
t/data/dbic_fixtures/350-RunLane.yml
t/data/dbic_fixtures/400-RunLaneStatus.yml
t/data/dbic_fixtures/400-RunStatus.yml
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/BustardSummary.xml
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#0_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#0_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#168_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#1_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#1_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#2_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#2_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#3_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane1/qc/8747_1#3_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#0_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#0_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#168_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#1_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#1_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#2_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#2_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#3_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#3_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#4_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#4_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#5_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#5_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#6_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane4/qc/8747_4#6_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#0_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#0_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#168_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#1_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#1_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#2_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#2_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#3_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#3_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#4_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#4_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#5_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#5_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#6_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/lane6/qc/8747_6#6_phix_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/qc/8747_4.spatial_filter.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/PB_cal_bam/archive/qc/8747_6.spatial_filter.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/InterOp/TileMetricsOut.bin
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/RunInfo.xml
t/data/example_runfolder/130917_MS6_10808_A_MS2030455-300V2/RunInfo.xml
t/data/example_runfolder/131010_HS34_11018_B_H722AADXX/RunInfo.xml
t/data/example_runfolder/131021_MS5_11123_A_MS2000187-150V3/RunInfo.xml
t/data/example_runfolder/151215_HS38_18472_A_H55HVADXX/Data/Intensities/BAM_basecalls_20151215-215034/metadata_cache_18472/npg/instrument/120.xml
t/data/example_runfolder/151215_HS38_18472_A_H55HVADXX/Data/Intensities/BAM_basecalls_20151215-215034/metadata_cache_18472/npg/run/18472.xml
t/data/example_runfolder/151215_HS38_18472_A_H55HVADXX/Data/Intensities/BAM_basecalls_20151215-215034/metadata_cache_18472/npg/run_status_dict.xml
t/data/example_runfolder/151215_HS38_18472_A_H55HVADXX/Data/Intensities/BAM_basecalls_20151215-215034/metadata_cache_18472/samplesheet_18472.csv
t/data/example_runfolder/151215_HS38_18472_A_H55HVADXX/RunInfo.xml
t/data/fix_configs/data_intensities_basecalls_config.xml
t/data/fix_configs/data_intensities_basecalls_diff_last_cycle_config.xml
t/data/fix_configs/data_intensities_config.xml
t/data/fix_configs/fixed_basecalls_config.xml
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