* update Hifiasm to version 0.19.5
  * update how Hifiasm outputs are compressed (bgz replacing gz), also
  * monitor hifiasm resources usage

  * update docker used in PBSV tasks to the version coming with official SMRTLink releases (2.9.0)
  * change how the 2-step PBSV process is done (following the recommended way now)

  * to version 2.0.7
  * using TRF bed
  * conditionally phase sv (requires phased bam)
  * generates its own vcf.gz and tbi

Overhaul how small variants are called in the WG pipelines

  * default to use DV to call small variants, Clair3 analysis needs to be requested explicitly
  * retire the Pepper toolchain completely from the CCS pipeline, using DV directly
  * for R10.4+ ONT data, also use DV directly
  * older ONT data would still use the PEPPER-DV-Margin pipeline
  * offers GPU version (though based on, it's not worth it yet)
  * update how bam haplotagging is done

Cleanup structural variants calling
  * experiment with SNF2 phasing SV calls (implicitly depends on small variants calling now)
  * tune PBSV calling
    - discover now supports --hifi
    - output vcf.gz and tbi
    - less verbose logging by default

Misc.:
  * optimizations to BAM merging and metrics workflow
  * updates coverage collection step
  * new R script to visualize log from vm_monitoring_script.sh

  * organize dockstore.yml file a bit

  * make WDL validation shell script more usable

  * update pbmm2 and pbindex to versions in SMRTLink

  * update GeneralUtils.wdl
    - two bash-like new tasks [CoerceMapToArrayOfPairs, CoerceArrayOfPairsToMap]
    - cleanup task CollapseArrayOfStrings

  * update resource allocations to tasks
    - NanoplotFromBam (also changes docker)
    - MosDepthWGS

  * incorporates gcloud cli (not just gsutil)
  * integrate libdeflate for more speedups

…sorted ONT bam

incorporate new tasks and optimize them

  * [CountMethylCallReads, GatherReadsWithoutMethylCalls]
    from sh_beans

  * [GetPileup, BamToRelevantPileup]
    from sh_more_atomic_qc

  * [GetReadGroupLines, GetSortOrder, SplitNameSortedUbam]
    from sh_ont_fc

  * [SamtoolsFlagStats, ParseFlagStatsJson]
    from sh_trvial_stats

  * [FilterBamByLen, InferSampleName]
    from sh_seqkit

  * [CountAlignmentRecords, StreamingBamErrored, CountAlignmentRecordsByFlag]
    from sh_maha_aln_metrics

  * [ResetSamplename]
    from sh_ingest_singlerg

  * [MergeBamsWithSamtools]
    from sh_ont_fc.Utils.wdl

  * [BamToFastq]
    from sh_more_bam_qcs
    and optimize it with
    sh_ingest_singlerg.Utils.wdl

delete
  * GetSortOrder as that's now implemented in GatherBamMetadata
  * Drop2304Alignments as that's no longer used

update dockers to the latest

CHERRY-PICK FROM VARIOUS QC/METRICS BRANCHES:

  * collect information about ML/MM tags in a long-read BAM
    (sh_beans)

  * a heuristic way to find peaks in a distribution (using dyst)
    (sh_dyst_peaker)

  * filter reads by length in a BAM
  * collect some read quality stats from (length-filtered) FASTQ/BAM
    (sh_seq_kit)

  * VerifyBamID2 (for contamination estimation)
  * naive sex-concordance check
    (sh_more_atomic_qc)

  * check fingerprint of a single BAM file
    (sh_sample_fp)

  * collect SAM flag stats
    (sh_trivial_stats)

  * make BeanCounter finalization optional
    (wdl/pipelines/TechAgnostic/Utility/CountTheBeans.wdl)
  * custom struct for sub-workflow config using a JSON
    (wdl/pipelines/TechAgnostic/Utility/LongReadsContaminationEstimation.wdl)
  * make fingerprint checking subworkflow control size filtering
    (wdl/tasks/QC/FPCheckAoU.wdl)
    (wdl/pipelines/TechAgnostic/Utility/VerifyBamFingerprint.wdl)
  * fix a warning by IDE/miniwdl complaining WDL stdlib function length only applies to Array
    (wdl/tasks/Utility/BAMutils.wdl)
  * various updates to Finalize
    (wdl/tasks/Utility/Finalize.wdl)

New tasks in (wdl/tasks/Utility/GeneralUtils.wdl) to
  * correctly convert Map to TSV
  * concatenate files

  * AlignAndCheckFingerprintCCS.wdl
  * CollectPacBioAlignedMetrics.wdl
  * CollectSMRTCellUnalignedMetrics.wdl

  (CHRRY-PICK & follow up to PR 406)

  * SampleLevelAlignedMetrics.wdl
  * PBCLRWholeGenome.wdl

  * new struct in AlignedBamQCandMetrics.wdl to facilicate as-sub-workflow calling
  * change parameters name for fingerprint workflows

  * make saving of reads without methylation SAM tags optional
  * better parameter naming

(affects contamination estimation)

… for efficiency

- Remove unnecessary BED file input from LongReadsContaminationEstimation workflow as BED paths are now hardcoded in the Docker image.
- Modify the inputs and commands in Contamination.wdl to align with new Docker setup and work with the .mu, .UD, and .bed files from the docker.
- Adjust workflow parameters to better reflect current data processing requirements and practices.

Removing SVDPrefix from the command line.