Sz dyst peaker #457
Open
Sz dyst peaker #457
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* 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
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
SaveRLArray.gcs_pathas a main outputsaveLRArrayOutputis available for copying to the Terra data table