##20251121.1
Exclude pod5 from delivery by default
Improve logging
Bugfix: Get all available samples in get_noindex_stats
Move Aviti Teton FlowcellPressureCheck directories into run directory before processing the run
Adapt analysis demultiplex-element to handle NULISA runs
Remove return as code was unreachable
Skip check for pod5/fast5 files
Skip toulligqc on ONT data if pod5/fast5 is missing
Add option to specify rsync options to NAS
Update Element analysis to handle AVITI24 Teton runs
Update Element analysis to handle NoIndex cases
Fix bug in link in Element flowcell status email
Update ONT transfer script to be instrument agnostic, more readable and resolve rrsync issues.
Fix bug in checking ONT run in statusdb
Add back missed FlowcellRunMetricsConnection check in statusdb
Replace the CouchDB package with IBM cloudant
Misc. improvements to ONT processing.
Bugfix: Fail organisation of ONT data if tar fails
Fix bug with ONT instrument identification
Adhere to function return format for error cases
Add URL to Element FCs in email notifications
Handle demux for Aviti runs with single samples
Cleanup of cleanup functions
Delay email warning about missing sample sheet for Illumina
Make it possible to "hide" old aviti runs from TACA in transfer log
Typo fix
Add instrument run on to bioinfodb to display on genstat
Bugfix for ONT ToulligQC, regarding detecting barcoded runs.
Have AVITI demux manifest accommodate samples with recipes of read length 0 by treating them as full length.
Fix command in ONT delivery
Improve testing CI
Improve logging for Aviti
Correction of help messages
Add feature to AVITI submanifest generation to tweak index mismatch thresholds if necessary.
Replace PR labels action
Improve the way TACA identifies run dirs in the "bioinfo_deliveries --update" command (bioinfo_tab.py).
Ruff formatting.
Do not run ToulligQC if its output directory can be found.
Email user instead of crashing if unable to create Illumina runobject
Fix for ONT demultiplexing status in bioinfo deliveries script
Add ONT instrument data to bioinfo_tab
No longer reserve PromethION column 3 for Clinical Genomics.
Change server_status nas to update statusdb by default
Add support for releasing DDS projects
Add support for uploading ONT data to DDS
Tweaks and bugfixes for ToulligQC.
Add automated QC reports with ToulligQC for ONT.
Add support for staging ONT data on Miarka
Add automated cleanup to ONT transfer script.
Add support for organising ONT data on Miarka
Add support for backing up Element Aviti data to PDC
Add exception handling for nonnumeric flowcell ids in bioinfo_tab
Add element instruments to bioinfo_tab
Fix extra postfix in sample names for BCL Convert
Fix missing settings for BCL Convert
Fix issue that index 2 is automatically converted to RC by BCL Convert
Fix small bug with Aviti transfer log
Add support for processing Element Aviti data
Fix TACA for handling 10X UMI cases by BCL Convert
Switch to tarball and skip compression
Update taca-ngi-pipeline repo URL in README
For re-demux: keep PDC archive date if exists
Update command used to run Anglerfish.
Add section header in samplesheet for run folder transfer
Improve CI for pipreqs check and pytest/codecov
Run mypy for entire repo regardless of depth.
Use run-specific name to find Anglerfish samplesheet.
Update server status to run on ngi-preproc
Fix erroneous name of pod5 output dir for ONT runs.
Broaden ONT transfer script's categorization of QC runs to either experiment dir or sample dir starting with "QC_".
Refine GHA VERSIONLOG.md check to compare to merge-base, not branch-base.
Expand test coverage by starting and checking demultiplexing for a NovaSeqXPlus run.
Include project IDs in the run folder tarball
Fix cases that MiSeq samplesheet misses index or index2
- Make sure TACA can handle runs that generate NO sequencing data at all
- Refactor logic of control function to reduce complexity
- Introduce custom Exception for quiet skipping (waiting on) runs
- Improve documentation
- Minor polishing of test to pass
Increase test coverage to 20%.
Implement CodeCoverage in CI.
Implement CI testing and increase testing coverage.
Fix bug with isinstance clause
Use abspath for Anglerfish stderr path, make it possible to instantiate ONT run w/o specifying the type, add more info to the ONT db update subcommand.
Fix bugs that changs in PR #404 were reverted in PR #411
Exclude pod5 dir and files from being copied to metadata dir.
Adapt ONT analysis to new ONT JSON format (also backwards compatible).
Update ONT instrument transfer script to ignore runs started in the 3rd PromethION column, which will be used by Clinical Genomics.
Run Anglerfish v0.6.0 with --lenient and --ont_barcodes options.
Version 1.0.0 (1) Support BCL Convert (2) Remove redundant codes and obsoleted platforms (3) Switch MiSeq to Illumina V3 samplesheet (4) Other refactors to improve performance
Fix bug with rsync permission issue cont.
Improve run_folder transfer
Fix bug with rsync permission issue
Fix functionality issues for Anglerfish launch by running via "conda run", fix erroneous file name reference and improve static typing.
Remove redundant cleanup_processing function in cleanup
Support multiple project ID for run folder transfer
Fix bug that NovaSeqXPlus date format cause error in writing pdc_archived timestamp
Remove the temp change of creating links
Supplement last PR, primary purpose is to differentiate user runs from QC runs in the instrument transfer script rather than the installed TACA.
Major overhaul of Nanopore stuff. Use generalized local script instead of installed TACA for both instruments and harmonize the way TACA handles Nanopore data from preprocessing. Implement automated handling of MinION QC runs.
Fix bugs for encrypting and archiving runs on ngi-preproc cont.
Fix bugs for encrypting and archiving runs on ngi-preproc
Adapt MinKNOW .json trimming to new format from Dorado update.
Allow manual database update of finished ONT runs
Add pandas to requiresments to accomodate last PR
Copy ONT metadata to ngi-nas-ns.
Update path to store Anglerfish results.
Implement logging for PromethION script.
Update handling of MinION QC runs to not run nanoseq, only anglerfish.
Update PromethION script to extend the scope of the log file parsing.
Enable TACA to retrieve error and warnings in bcl2fastq logs
Update PromethION script to run rsync w. -u flag and clarify archiving code.
Let PromethION script search through device logs to dump flow cell pore count history into the run dir.
Rework how PromethION script detects runs to catch mis-named ones, too.
Add support for NovaSeqXPlus and improve readability
Add functionality to update DB of specified run dirs.
Trim out unused data acquisition outputs from ONT report .json files before sending them to CouchDB.
Add storage_systems to server_status command to allow disk space surveillance of mounted virtual NAS:es. Also added Dockerfile and devcontainer setup.
Change how MinKNOW reports are synced to GenStat server to increase traceability and enable transfer of the reports of finished runs.
Enforce MinKNOW reports retain MinKNOW run ID upon transfer to ngi-internal. Improve logging.
Change offload location in promethion_transfer.py
Use a hidden file to indicate when the final rsync of ONT data to ngi-nas is done
Move MinKNOW reports to ngi-internal instead of embedding in StatusDB doc
Handle demux case that ordered read length is different from seq setup
##20230213.1 Further updates to ONT runs TACA <-> CouchDB interplay after local troubleshooting. Improve code readability, logging and exception handling.
##20230207.1 Add functionality for monitoring PromethION status
##20230117.2 More robust handling of ONT transfers
##20230117.1 Integrate ONT data flow with CouchDB nanopore_runs
##20221102.1 Include MinION data in transfer to HPC cluster
##20221028.1 Cleaner check for ONT transfer destination
##20221011.1 Add versioning for PromethION offload script
##20220830.1 Change promethion directory levels
Set short single index to 8nt
Updates to promethion offload script
Include promethion offload script
##20220610.1 Convert statusdb urls to https
Handle special demux for NoIndex cases
Include index list from undet of complex lanes
Support addtional 10X index types
Allow 0 mismatch in demux for short single index for MiSeq
Bug fix and refactor handling for 10X indexes
Handle cases with different UMI lengths
Add promethion to server_status
Small refactor for NoIndex
Change cleanup irma to cleanup miarka
Remove "Irma" from email/log
Re-define signal for sequencing done
Refactor cleanup_nas
Fix bug that samplesheet of MiSeq is overwritten
Change samplesheet location for MiSeq
Add option for syncing MinION delivery data to storage
Updates for compability with nanoseq v2.0.1
Only process MinION QC runs
Refactor of MinION code
Specify CopyComplete.txt as indicator for cleaning NovaSeq runs
Allow 0 mismatch in demux for short single index
Handle special case with index 2 only for NovaSeq
Support addtional 10X index types
Handle special case with index 2 only
Small adjust of 10X ATACseq masks
Support different FC ID pattern for NextSeq2000 in bioinfo_tab.py
Support different FC ID pattern for NextSeq2000
Support addtional 10X index types
Fix bug that runtype was overwritten
Fix FC name pattern for NextSeq2000
Setup VERSIONLOG.md