From 2a109f7dfbcec8678c5fdd7201234249e89f5cea Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 5 Jan 2024 18:25:25 +0000 Subject: [PATCH 1/2] Use one aggregation method for merges. Use st::api::lims->aggregate_libraries() method for both 'merge_lanes' and 'merge_by_library' pipeline options. --- MANIFEST | 114 +++++++----------- lib/npg_pipeline/base.pm | 97 +++++++++------ t/10-base.t | 3 +- t/10-runfolder_scaffold.t | 24 ++-- t/15-product-release.t | 12 +- .../no_cal/archive/README | 6 + .../plex0/.npg_cache_10000/26291_1#0_1.fastq} | 0 .../plex0/.npg_cache_10000/26291_1#0_2.fastq} | 0 .../26291#0.bai => lane1/plex0/26291_1#0.bai} | 0 .../26291#0.bam => lane1/plex0/26291_1#0.bam} | 0 .../plex0/26291_1#0.bam.md5} | 0 .../plex0/26291_1#0.bam_stats} | 0 .../plex0/26291_1#0.cram} | 0 .../plex0/26291_1#0.cram.crai} | 0 .../plex0/26291_1#0.cram.md5} | 0 .../plex0/26291_1#0.flagstat} | 0 .../plex0/26291_1#0.orig.seqchksum} | 0 .../plex0/26291_1#0.seqchksum} | 0 .../26291_1#0.sha512primesums512.seqchksum} | 0 .../plex0/26291_1#0.spatial_filter.stats} | 0 .../plex0/26291_1#0_F0x900.stats} | 0 .../plex0/26291_1#0_F0xB00.stats} | 0 .../plex0/26291_1#0_phix.bai} | 0 .../plex0/26291_1#0_phix.bam} | 0 .../plex0/26291_1#0_phix.bam.md5} | 0 .../plex0/26291_1#0_phix.bam_stats} | 0 .../plex0/26291_1#0_phix.cram} | 0 .../plex0/26291_1#0_phix.cram.crai} | 0 .../plex0/26291_1#0_phix.cram.md5} | 0 .../plex0/26291_1#0_phix.flagstat} | 0 .../26291_1#0_phix.markdups_metrics.txt} | 0 .../plex0/26291_1#0_phix.seqchksum} | 0 ...291_1#0_phix.sha512primesums512.seqchksum} | 0 .../plex0/26291_1#0_phix_F0x900.stats} | 0 .../plex0/26291_1#0_phix_F0xB00.stats} | 0 .../26291_1#0.alignment_filter_metrics.json} | 0 .../plex0/qc/26291_1#0.bam_flagstats.json} | 0 .../plex0/qc/26291_1#0.gc_fraction.json} | 0 .../plex0/qc/26291_1#0.insert_size.json} | 0 .../plex0/qc/26291_1#0.qX_yield.json} | 0 .../plex0/qc/26291_1#0.ref_match.json} | 0 .../plex0/qc/26291_1#0.sequence_error.json} | 0 .../plex0/qc/26291_1#0.sequence_summary.json} | 0 .../qc/26291_1#0_F0x900.samtools_stats.json} | 0 .../qc/26291_1#0_F0xB00.samtools_stats.json} | 0 .../qc/26291_1#0_phix.bam_flagstats.json} | 0 .../qc/26291_1#0_phix.sequence_summary.json} | 0 ...26291_1#0_phix_F0x900.samtools_stats.json} | 0 ...26291_1#0_phix_F0xB00.samtools_stats.json} | 0 .../.npg_cache_10000/26291#888_1.fastq | 0 .../.npg_cache_10000/26291#888_2.fastq | 0 .../no_cal/archive/plex888/26291#888.bai | 0 .../no_cal/archive/plex888/26291#888.bam | 0 .../no_cal/archive/plex888/26291#888.bam.md5 | 1 - .../archive/plex888/26291#888.bam_stats | 0 .../no_cal/archive/plex888/26291#888.cram | 0 .../archive/plex888/26291#888.cram.crai | 0 .../no_cal/archive/plex888/26291#888.cram.md5 | 1 - .../no_cal/archive/plex888/26291#888.flagstat | 0 .../plex888/26291#888.markdups_metrics.txt | 0 .../archive/plex888/26291#888.orig.seqchksum | 0 .../archive/plex888/26291#888.seqchksum | 0 .../26291#888.sha512primesums512.seqchksum | 0 .../plex888/26291#888.spatial_filter.stats | 0 .../archive/plex888/26291#888_F0x900.stats | 0 .../archive/plex888/26291#888_F0xB00.stats | 0 .../archive/plex888/qc/26291#888.adapter.json | 0 .../plex888/qc/26291#888.bam_flagstats.json | 0 .../plex888/qc/26291#888.gc_fraction.json | 0 .../plex888/qc/26291#888.insert_size.json | 0 .../plex888/qc/26291#888.qX_yield.json | 0 .../plex888/qc/26291#888.ref_match.json | 0 .../plex888/qc/26291#888.sequence_error.json | 0 .../qc/26291#888.sequence_summary.json | 0 .../qc/26291#888_F0x900.samtools_stats.json | 0 .../qc/26291#888_F0xB00.samtools_stats.json | 0 76 files changed, 135 insertions(+), 123 deletions(-) create mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/README rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/.npg_cache_10000/26291#0_1.fastq => lane1/plex0/.npg_cache_10000/26291_1#0_1.fastq} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/.npg_cache_10000/26291#0_2.fastq => lane1/plex0/.npg_cache_10000/26291_1#0_2.fastq} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.bai => lane1/plex0/26291_1#0.bai} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.bam => lane1/plex0/26291_1#0.bam} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.bam.md5 => lane1/plex0/26291_1#0.bam.md5} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.bam_stats => lane1/plex0/26291_1#0.bam_stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.cram => lane1/plex0/26291_1#0.cram} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.cram.crai => lane1/plex0/26291_1#0.cram.crai} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.cram.md5 => lane1/plex0/26291_1#0.cram.md5} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.flagstat => lane1/plex0/26291_1#0.flagstat} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.orig.seqchksum => lane1/plex0/26291_1#0.orig.seqchksum} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.seqchksum => lane1/plex0/26291_1#0.seqchksum} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.sha512primesums512.seqchksum => lane1/plex0/26291_1#0.sha512primesums512.seqchksum} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0.spatial_filter.stats => lane1/plex0/26291_1#0.spatial_filter.stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_F0x900.stats => lane1/plex0/26291_1#0_F0x900.stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_F0xB00.stats => lane1/plex0/26291_1#0_F0xB00.stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.bai => lane1/plex0/26291_1#0_phix.bai} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.bam => lane1/plex0/26291_1#0_phix.bam} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.bam.md5 => lane1/plex0/26291_1#0_phix.bam.md5} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.bam_stats => lane1/plex0/26291_1#0_phix.bam_stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.cram => lane1/plex0/26291_1#0_phix.cram} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.cram.crai => lane1/plex0/26291_1#0_phix.cram.crai} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.cram.md5 => lane1/plex0/26291_1#0_phix.cram.md5} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.flagstat => lane1/plex0/26291_1#0_phix.flagstat} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.markdups_metrics.txt => lane1/plex0/26291_1#0_phix.markdups_metrics.txt} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.seqchksum => lane1/plex0/26291_1#0_phix.seqchksum} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix.sha512primesums512.seqchksum => lane1/plex0/26291_1#0_phix.sha512primesums512.seqchksum} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix_F0x900.stats => lane1/plex0/26291_1#0_phix_F0x900.stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/26291#0_phix_F0xB00.stats => lane1/plex0/26291_1#0_phix_F0xB00.stats} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.alignment_filter_metrics.json => lane1/plex0/qc/26291_1#0.alignment_filter_metrics.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.bam_flagstats.json => lane1/plex0/qc/26291_1#0.bam_flagstats.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.gc_fraction.json => lane1/plex0/qc/26291_1#0.gc_fraction.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.insert_size.json => lane1/plex0/qc/26291_1#0.insert_size.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.qX_yield.json => lane1/plex0/qc/26291_1#0.qX_yield.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.ref_match.json => lane1/plex0/qc/26291_1#0.ref_match.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.sequence_error.json => lane1/plex0/qc/26291_1#0.sequence_error.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0.sequence_summary.json => lane1/plex0/qc/26291_1#0.sequence_summary.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_F0x900.samtools_stats.json => lane1/plex0/qc/26291_1#0_F0x900.samtools_stats.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_F0xB00.samtools_stats.json => lane1/plex0/qc/26291_1#0_F0xB00.samtools_stats.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_phix.bam_flagstats.json => lane1/plex0/qc/26291_1#0_phix.bam_flagstats.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_phix.sequence_summary.json => lane1/plex0/qc/26291_1#0_phix.sequence_summary.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_phix_F0x900.samtools_stats.json => lane1/plex0/qc/26291_1#0_phix_F0x900.samtools_stats.json} (100%) rename t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/{plex0/qc/26291#0_phix_F0xB00.samtools_stats.json => lane1/plex0/qc/26291_1#0_phix_F0xB00.samtools_stats.json} (100%) delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/.npg_cache_10000/26291#888_1.fastq delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/.npg_cache_10000/26291#888_2.fastq delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bai delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam.md5 delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam_stats delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram.crai delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram.md5 delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.flagstat delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.markdups_metrics.txt delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.orig.seqchksum delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.seqchksum delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.sha512primesums512.seqchksum delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.spatial_filter.stats delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888_F0x900.stats delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888_F0xB00.stats delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.adapter.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.bam_flagstats.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.gc_fraction.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.insert_size.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.qX_yield.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.ref_match.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.sequence_error.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.sequence_summary.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888_F0x900.samtools_stats.json delete mode 100644 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888_F0xB00.samtools_stats.json diff --git a/MANIFEST b/MANIFEST index e5027ee97..0606f6ba8 100644 --- a/MANIFEST +++ b/MANIFEST @@ -286,6 +286,7 @@ t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_2018 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/26291_2#9.bam t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/26291_2.spatial_filter t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/26291_2.stats +t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/README 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+t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/qc/26291_1#0_phix_F0x900.samtools_stats.json +t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/qc/26291_1#0_phix_F0xB00.samtools_stats.json t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex1/.npg_cache_10000/26291#1_1.fastq t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex1/.npg_cache_10000/26291#1_2.fastq t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex1/26291#1.bai @@ -935,33 +936,6 @@ t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_2018 t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex8/qc/26291#8_phix.sequence_summary.json t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex8/qc/26291#8_phix_F0x900.samtools_stats.json t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex8/qc/26291#8_phix_F0xB00.samtools_stats.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/.npg_cache_10000/26291#888_1.fastq -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/.npg_cache_10000/26291#888_2.fastq -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bai -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam.md5 -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.bam_stats -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram.crai -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.cram.md5 -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.flagstat -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.markdups_metrics.txt -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.orig.seqchksum -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.seqchksum -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.sha512primesums512.seqchksum -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888.spatial_filter.stats -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888_F0x900.stats -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/26291#888_F0xB00.stats -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.adapter.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.bam_flagstats.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.gc_fraction.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.insert_size.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.qX_yield.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.ref_match.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.sequence_error.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888.sequence_summary.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888_F0x900.samtools_stats.json -t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex888/qc/26291#888_F0xB00.samtools_stats.json t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex9/.npg_cache_10000/26291#9_1.fastq t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex9/.npg_cache_10000/26291#9_2.fastq t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex9/26291#9.bai diff --git a/lib/npg_pipeline/base.pm b/lib/npg_pipeline/base.pm index 0fe98efbf..a4c28161f 100644 --- a/lib/npg_pipeline/base.pm +++ b/lib/npg_pipeline/base.pm @@ -5,7 +5,7 @@ use namespace::autoclean; use MooseX::Getopt::Meta::Attribute::Trait::NoGetopt; use POSIX qw(strftime); use Math::Random::Secure qw{irand}; -use List::MoreUtils qw{any}; +use List::MoreUtils qw{any uniq}; use File::Basename; use Readonly; @@ -358,49 +358,51 @@ sub _build_products { if ($self->has_product_rpt_list) { @data_lims = ($self->lims); } else { - my @positions = $self->positions; - @lane_lims = map { $self->lims4lane($_) } @positions; + @lane_lims = map { $self->lims4lane($_) } $self->positions; - if ($self->merge_lanes) { - @data_lims = $self->lims->aggregate_xlanes(@positions); - } else { + my %tag0_lims = (); + if ($self->is_indexed) { + %tag0_lims = map { $_->position => $_->create_tag_zero_object() } + grep { $_->is_pool } @lane_lims; + } + + if ($self->merge_lanes || $self->merge_by_library) { + + my $all_lims = $self->lims->aggregate_libraries(\@lane_lims); + @data_lims = @{$all_lims->{'singles'}}; # Might be empty. - my %tag0_lims = (); - if ($self->is_indexed) { - %tag0_lims = map { $_->position => $_->create_tag_zero_object() } - grep { $_->is_pool } @lane_lims; + # merge_lanes option implies a merge across all lanes. + if ($self->merge_lanes && (@lane_lims > 1)) { + $self->_check_lane_merge_is_viable( + \@lane_lims, $all_lims->{'singles'}, $all_lims->{'merges'}); } - if ($self->merge_by_library) { - my $all_lims = $self->lims->aggregate_libraries(\@lane_lims); - @data_lims = @{$all_lims->{'singles'}}; # Might be empty. - # Tag zero LIMS objects for all lanes, merged or unmerged. - push @data_lims, map { $tag0_lims{$_} } (sort keys %tag0_lims); - - if ( @{$all_lims->{'merges'}} ) { - # If the libraries are merged across a subset of lanes under analysis, - # the 'selected_lanes' flag needs to be flipped to true. - if (!$self->_selected_lanes) { - my $rpt_list = $all_lims->{'merges'}->[0]->rpt_list;; - my $num_components = - npg_tracking::glossary::composition::factory::rpt_list - ->new(rpt_list => $rpt_list) - ->create_composition()->num_components(); - if ($num_components != scalar @lane_lims) { - $self->_set_selected_lanes(1); - } + # Tag zero LIMS objects for all pooled lanes, merged or unmerged. + push @data_lims, map { $tag0_lims{$_} } (sort keys %tag0_lims); + + if ( @{$all_lims->{'merges'}} ) { + # If the libraries are merged across a subset of lanes under analysis, + # the 'selected_lanes' flag needs to be flipped to true. + if (!$self->_selected_lanes) { + my $rpt_list = $all_lims->{'merges'}->[0]->rpt_list;; + my $num_components = + npg_tracking::glossary::composition::factory::rpt_list + ->new(rpt_list => $rpt_list) + ->create_composition()->num_components(); + if ($num_components != scalar @lane_lims) { + $self->_set_selected_lanes(1); } - push @data_lims, @{$all_lims->{'merges'}}; } + push @data_lims, @{$all_lims->{'merges'}}; + } - } else { - # To keep backward-compatible order of pipeline invocations, add - # tag zero LIMS object at the end of other objects for the lane. - @data_lims = map { - exists $tag0_lims{$_->position} ? + } else { + # To keep backward-compatible order of pipeline invocations, add + # tag zero LIMS object at the end of other objects for the lane. + @data_lims = map { + exists $tag0_lims{$_->position} ? ($_->children, $tag0_lims{$_->position}) : $_ - } @lane_lims; - } + } @lane_lims; } } @@ -442,6 +444,29 @@ sub _lims_object2product { ); } +sub _check_lane_merge_is_viable { + my ($self, $lane_lims, $singles, $merges) = @_; + + my @num_plexes = uniq + map { scalar @{$_} } + map { [grep { !$_->is_control } @{$_}] } + map { [$_->children()] } @{$lane_lims}; + + my $m = 'merge_lane option is not viable: '; + if (@num_plexes > 1) { + $self->logcroak($m . 'different number of samples in lanes'); + } + if (any { !$_->is_control } @{$singles}) { + $self->logcroak($m . 'unmerged samples are present after aggregation'); + } + if (@{$merges} != $num_plexes[0]) { + $self->logcroak($m . 'number of merged samples after aggregation ' . + 'differs from the number of samples in a lane'); + } + + return 1; +} + __PACKAGE__->meta->make_immutable; 1; diff --git a/t/10-base.t b/t/10-base.t index ab83edcc4..ec648467c 100644 --- a/t/10-base.t +++ b/t/10-base.t @@ -96,13 +96,14 @@ subtest 'products - merging (or not) lanes' => sub { local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; cp 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + cp 't/data/novaseq/210111_A00513_0447_AHJ55JDSXY/RunInfo.xml', "$rf_path/RunInfo.xml"; $b = npg_pipeline::base->new(runfolder_path => $rf_path, id_run => 999); ok ($b->merge_lanes, 'merge_lanes flag is set'); lives_ok {$products = $b->products} 'products hash created for NovaSeq run'; ok (exists $products->{'lanes'}, 'products lanes key exists'); is (scalar @{$products->{'lanes'}}, 4, 'four lane product'); ok (exists $products->{'data_products'}, 'products data_products key exists'); - is (scalar @{$products->{'data_products'}}, 23, '23 data products'); + is (scalar @{$products->{'data_products'}}, 29, '29 data products'); local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_rapidrun_nopool.csv'; cp 't/data/run_params/runParameters.hiseq.rr.xml', "$rf_path/runParameters.xml"; diff --git a/t/10-runfolder_scaffold.t b/t/10-runfolder_scaffold.t index 47c6c1415..880d1abf3 100644 --- a/t/10-runfolder_scaffold.t +++ b/t/10-runfolder_scaffold.t @@ -67,12 +67,13 @@ subtest 'top level scaffold' => sub { }; subtest 'product level scaffold, NovaSeq all lanes' => sub { - plan tests => 99; + plan tests => 101; my $util = t::util->new(); my $rfh = $util->create_runfolder(); my $rf_path = $rfh->{'runfolder_path'}; - fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/novaseq/210111_A00513_0447_AHJ55JDSXY/RunInfo.xml', "$rf_path/RunInfo.xml"; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; my $rfs = Moose::Meta::Class->create_anon_class( @@ -95,6 +96,8 @@ subtest 'product level scaffold, NovaSeq all lanes' => sub { push @dirs, (map {join q[/], $_, 'qc'} @original); push @dirs, (map {join q[/], $_, 'tileviz_'.$_} @original); push @dirs, (map {join q[/], $_, '.npg_cache_10000'} @original); + push @dirs, (map {join q[/], $_, 'plex0/qc'} @original); + push @dirs, (map {join q[/], $_, 'plex888/qc'} @original); map { ok (-d $_, "$_ created") } map {join q[/], $apath, $_} @dirs; for my $lane (@original) { @@ -106,7 +109,7 @@ subtest 'product level scaffold, NovaSeq all lanes' => sub { like ($content, qr/No tileviz data available for this lane/, 'info exists'); } - @original = map {'plex' . $_} (0 .. 21, 888); + @original = map {'plex' . $_} (1 .. 21); @dirs = @original; push @dirs, (map {join q[/], $_, 'qc'} @original); push @dirs, (map {join q[/], $_, '.npg_cache_10000'} @original); @@ -115,16 +118,17 @@ subtest 'product level scaffold, NovaSeq all lanes' => sub { my $tileviz_index = join q[/], $apath, 'tileviz', 'index.html'; ok (-e $tileviz_index, 'tileviz index created'); my @lines = read_file($tileviz_index); - is (scalar @lines, 7, 'tileviz index contains sevel lines'); + is (scalar @lines, 7, 'tileviz index contains seven lines'); }; subtest 'product level scaffold, NovaSeq selected lanes' => sub { - plan tests => 175; + plan tests => 165; my $util = t::util->new(); my $rfh = $util->create_runfolder(); my $rf_path = $rfh->{'runfolder_path'}; - fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/run_params/runParameters.novaseq.xml', "$rf_path/runParameters.xml"; + fcopy 't/data/novaseq/210111_A00513_0447_AHJ55JDSXY/RunInfo.xml', "$rf_path/RunInfo.xml"; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/products/samplesheet_novaseq4lanes.csv'; my $rfs = Moose::Meta::Class->create_anon_class( @@ -149,12 +153,14 @@ subtest 'product level scaffold, NovaSeq selected lanes' => sub { push @dirs, (map {join q[/], $_, 'qc'} @original); push @dirs, (map {join q[/], $_, 'tileviz_'.$_} @original); push @dirs, (map {join q[/], $_, '.npg_cache_10000'} @original); + push @dirs, (map {join q[/], $_, 'plex0/qc'} @original); + push @dirs, (map {join q[/], $_, 'plex888/qc'} @original); map { ok (-d $_, "$_ created") } map {join q[/], $apath, $_} @dirs; @dirs = qw/lane1 lane4/; map { ok (!-e $_, "$_ not created") } map {join q[/], $apath, $_} @dirs; - @original = map {'lane2-3/plex' . $_} (0 .. 21, 888); + @original = map {'lane2-3/plex' . $_} (1 .. 21); @dirs = @original; push @dirs, (map {join q[/], $_, 'qc'} @original); push @dirs, (map {join q[/], $_, '.npg_cache_10000'} @original); @@ -172,7 +178,7 @@ subtest 'product level scaffold, NovaSeq selected lanes' => sub { "link for lane $l file is not created"); } - for my $t ( (0 .. 21, 888) ) { + for my $t ( (1 .. 21) ) { my $name = "999_2-3#${t}.cram"; my $file = "$napath/lane2-3/plex${t}/stage1/$name"; ok ((-l $file), "link for plex $t is created"); @@ -252,4 +258,4 @@ subtest 'product level scaffold, library merge for NovaSeqX' => sub { } }; -1; \ No newline at end of file +1; diff --git a/t/15-product-release.t b/t/15-product-release.t index cf3901e11..aef2e7f69 100644 --- a/t/15-product-release.t +++ b/t/15-product-release.t @@ -43,7 +43,7 @@ my $runfolder_path = 't/data/novaseq/180709_A00538_0010_BH3FCMDRXX'; my $timestamp = '20180701-123456'; subtest 'expected_files' => sub { - plan tests => 1; + plan tests => 2; my $archiver = $cls->new_object (conf_path => "t/data/release/config/archive_on", @@ -52,10 +52,11 @@ subtest 'expected_files' => sub { timestamp => $timestamp, qc_schema => $qc); - my $product = shift @{$archiver->products->{data_products}}; - my $path = "$runfolder_path/Data/Intensities/" . 'BAM_basecalls_20180805-013153/no_cal/archive/plex1'; + my $product = $archiver->products->{data_products}->[4]; + is ($product->rpt_list, '26291:1:1;26291:2:1', 'correct product'); + my @expected = sort map { "$path/$_" } ('26291#1_F0x900.stats', '26291#1_F0xB00.stats', @@ -88,8 +89,7 @@ subtest 'expected_unaligned_files' => sub { timestamp => $timestamp, qc_schema => $qc); - my $product = shift @{$archiver->products->{data_products}}; - + my $product = $archiver->products->{data_products}->[4]; my $path = "$runfolder_path/Data/Intensities/" . 'BAM_basecalls_20180805-013153/no_cal/archive/plex1'; my @expected = sort map { "$path/$_" } @@ -105,3 +105,5 @@ subtest 'expected_unaligned_files' => sub { diag explain \@observed; }; +1; + diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/README b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/README new file mode 100644 index 000000000..b673710b9 --- /dev/null +++ b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/README @@ -0,0 +1,6 @@ +5 January 2024 + +Both lane1 and lane2 directories are expected to contain +subdirectories plex0 and plex888 with all relevant files +and subdirectories. Only lane1/plex0 directory is present +in this testrunfolder as a representative example. diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/.npg_cache_10000/26291#0_1.fastq b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/.npg_cache_10000/26291_1#0_1.fastq similarity index 100% rename from t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/.npg_cache_10000/26291#0_1.fastq rename to t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/.npg_cache_10000/26291_1#0_1.fastq diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/.npg_cache_10000/26291#0_2.fastq b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/.npg_cache_10000/26291_1#0_2.fastq similarity index 100% rename from t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/.npg_cache_10000/26291#0_2.fastq rename to t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/.npg_cache_10000/26291_1#0_2.fastq diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/26291#0.bai b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/26291_1#0.bai similarity index 100% rename from t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/26291#0.bai rename to t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/26291_1#0.bai diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/26291#0.bam b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/26291_1#0.bam similarity index 100% rename from t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/26291#0.bam rename to t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/26291_1#0.bam diff --git a/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/plex0/26291#0.bam.md5 b/t/data/novaseq/180709_A00538_0010_BH3FCMDRXX/Data/Intensities/BAM_basecalls_20180805-013153/no_cal/archive/lane1/plex0/26291_1#0.bam.md5 similarity 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fd5477972db94197737c673726ba989fb5e5c736 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 9 Jan 2024 18:32:29 +0000 Subject: [PATCH 2/2] Described the change --- Changes | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/Changes b/Changes index 28b2b586a..f587b727e 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,16 @@ LIST OF CHANGES --------------- + - Use st::api::lims->aggregate_libraries() method for both 'merge_lanes' and + 'merge_by_library' pipeline options. This is a breaking change as far as + archival and deletion of NovaSeq Standard workflow data is concerned. + Key change for lane merging for this data will be that tag 0 and tag 888 will + not be merged across the lanes. + The NovaSeq Standard workflow, where there is only one input port, is + different to the more general merging across lanes where the (claimed) same + library has been sequenced. But this is not a valid reason to maintain separate + code. + release 67.1.1 - Fixed correct pp collection root for MiSeq