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.travis.yml
bin/npg_heron_metadata_upload
bin/npg_pipeline_analysis_runner
bin/npg_pipeline_archival_runner
bin/npg_pipeline_central
bin/npg_pipeline_check_cluster_count
bin/npg_pipeline_create_summary_link
bin/npg_pipeline_execute_saved_command
bin/npg_pipeline_job_env_to_threads
bin/npg_pipeline_notify_delivery
bin/npg_pipeline_post_qc_review
bin/npg_pipeline_preexec_references
bin/npg_pipeline_script_must_be_unique_runner
bin/npg_pipeline_seqchksum_comparator
bin/npg_receipt4run_is_deletable
bin/npg_run_is_deletable
Build.PL
Changes
data/config_files/function_list_central.json
data/config_files/function_list_central.json.png
data/config_files/function_list_central_qc_run.json
data/config_files/function_list_central_qc_run.json.png
data/config_files/function_list_post_qc_review.json
data/config_files/function_list_post_qc_review.json.png
data/config_files/function_list_post_run_archived.json
data/config_files/function_list_post_run_archived.json.png
data/config_files/general_values.ini
data/config_files/lsf.ini
data/config_files/wr.json
lib/npg_pipeline/base.pm
lib/npg_pipeline/base/options.pm
lib/npg_pipeline/cache.pm
lib/npg_pipeline/cache/barcodes.pm
lib/npg_pipeline/cache/reference.pm
lib/npg_pipeline/cache/reference/constants.pm
lib/npg_pipeline/daemon.pm
lib/npg_pipeline/daemon/analysis.pm
lib/npg_pipeline/daemon/archival.pm
lib/npg_pipeline/executor.pm
lib/npg_pipeline/executor/lsf.pm
lib/npg_pipeline/executor/lsf/job.pm
lib/npg_pipeline/executor/options.pm
lib/npg_pipeline/executor/wr.pm
lib/npg_pipeline/function/autoqc.pm
lib/npg_pipeline/function/autoqc_archiver.pm
lib/npg_pipeline/function/bqsr_calc.pm
lib/npg_pipeline/function/cache_merge_component.pm
lib/npg_pipeline/function/cluster_count.pm
lib/npg_pipeline/function/current_analysis_link.pm
lib/npg_pipeline/function/definition.pm
lib/npg_pipeline/function/haplotype_caller.pm
lib/npg_pipeline/function/log_files_archiver.pm
lib/npg_pipeline/function/merge_recompress.pm
lib/npg_pipeline/function/p4_stage1_analysis.pm
lib/npg_pipeline/function/stage2pp.pm
lib/npg_pipeline/function/pp_archiver.pm
lib/npg_pipeline/function/product_delivery_notifier.pm
lib/npg_pipeline/function/run_data_to_irods_archiver.pm
lib/npg_pipeline/function/s3_archiver.pm
lib/npg_pipeline/function/seq_alignment.pm
lib/npg_pipeline/function/seq_to_irods_archiver.pm
lib/npg_pipeline/function/seqchksum_comparator.pm
lib/npg_pipeline/function/start_stop.pm
lib/npg_pipeline/function/status.pm
lib/npg_pipeline/function/util.pm
lib/npg_pipeline/function/warehouse_archiver.pm
lib/npg_pipeline/pluggable.pm
lib/npg_pipeline/pluggable/central.pm
lib/npg_pipeline/pluggable/registry.pm
lib/npg_pipeline/product.pm
lib/npg_pipeline/product/cache_merge.pm
lib/npg_pipeline/product/chunk.pm
lib/npg_pipeline/product/heron/upload/library.pm
lib/npg_pipeline/product/heron/upload/metadata_client.pm
lib/npg_pipeline/product/heron/upload/run.pm
lib/npg_pipeline/product/release.pm
lib/npg_pipeline/product/release/irods.pm
lib/npg_pipeline/product/release/portable_pipeline.pm
lib/npg_pipeline/runfolder_scaffold.pm
lib/npg_pipeline/validation.pm
lib/npg_pipeline/validation/autoqc.pm
lib/npg_pipeline/validation/common.pm
lib/npg_pipeline/validation/entity.pm
lib/npg_pipeline/validation/irods.pm
lib/npg_pipeline/validation/s3.pm
lib/npg_tracking/daemon/analysis.pm
lib/npg_tracking/daemon/archival.pm
MANIFEST This list of files
README
README.md
scripts/jgf2gml
scripts/travis_install.sh
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-barcodes.t
t/10-cache.t
t/10-pluggable-central.t
t/10-pluggable-registry.t
t/10-pluggable.t
t/10-product.t
t/10-runfolder_scaffold.t
t/10-script-job_env_to_threads.t
t/10-validation-autoqc.t
t/10-validation-entity.t
t/10-validation-irods.t
t/10-validation-s3.t
t/10-validation.t
t/15-pipeline_launcher_scripts.t
t/15-product-heron-upload-metadata.t
t/15-product-release.t
t/20-function-autoqc.t
t/20-function-autoqc_archiver.t
t/20-function-bqsr_calc.t
t/20-function-cache_merge_component.t
t/20-function-cluster_count.t
t/20-function-current_analysis_link.t
t/20-function-definition.t
t/20-function-haplotype_caller.t
t/20-function-log_files_archiver.t
t/20-function-merge_recompress.t
t/20-function-p4_stage1_analysis.t
t/20-function-stage2pp.t
t/20-function-pp_archiver.t
t/20-function-product_delivery_notifier.t
t/20-function-run_data_to_irods_archiver.t
t/20-function-s3_archiver.t
t/20-function-seq_alignment.t
t/20-function-seq_to_irods_archiver.t
t/20-function-seqchksum_comparator.t
t/20-function-start_stop.t
t/20-function-status.t
t/20-function-warehouse_archiver.t
t/30-executor-lsf-job.t
t/30-executor-lsf.t
t/30-executor-wr.t
t/30-executor.t
t/50-npg_pipeline-daemon-analysis.t
t/50-npg_pipeline-daemon-archival.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/machine-location
t/bin/machine-location
t/bin/red/machine-location
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/barcodes/samplesheet_batch2015.csv
t/data/barcodes/samplesheet_batch42225.csv
t/data/barcodes/samplesheet_batch42225_amended1.csv
t/data/barcodes/samplesheet_batch42225_amended2.csv
t/data/barcodes/samplesheet_batch5378.csv
t/data/barcodes/samplesheet_batch6532.csv
t/data/barcodes/samplesheet_batch6713.csv
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/eight_reads.cram
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane1/8747_bfs_fofn.txt
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane1/8747_sf_fofn.txt
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane1/qc/8747_1#0_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane1/qc/8747_1#168_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane1/qc/8747_1#1_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane1/qc/8747_1#2_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane1/qc/8747_1#3_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/8747_bfs_fofn.txt
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane4/8747_sf_fofn.txt
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane4/qc/8747_4#0_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#168_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/archive/lane4/qc/8747_4#1_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#2_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#3_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#4_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#5_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4#6_bam_flagstats.json
t/data/example_runfolder/121103_HS29_08747_B_C1BV5ACXX/Data/Intensities/BAM_basecalls_20130122-085552/no_cal/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/no_cal/archive/lane4/qc/8747_4.spatial_filter.json
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