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VERSIONLOG.md

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TACA Version Log

20241108.1

Add element instruments to bioinfo_tab

20241031.1

Fix extra postfix in sample names for BCL Convert

20241029.3

Fix missing settings for BCL Convert

20241029.2

Fix issue that index 2 is automatically converted to RC by BCL Convert

20241029.1

Fix small bug with Aviti transfer log

20241025.1

Add support for processing Element Aviti data

20241024.1

Fix TACA for handling 10X UMI cases by BCL Convert

20241016.1

Switch to tarball and skip compression

20241007.1

Update taca-ngi-pipeline repo URL in README

20240927.1

For re-demux: keep PDC archive date if exists

20240816.1

Update command used to run Anglerfish.

20240705.1

Add section header in samplesheet for run folder transfer

20240701.1

Improve CI for pipreqs check and pytest/codecov

20240617.1

Run mypy for entire repo regardless of depth.

20240527.1

Use run-specific name to find Anglerfish samplesheet.

20240523.1

Update server status to run on ngi-preproc

20240520.1

Fix erroneous name of pod5 output dir for ONT runs.

20240507.1

Broaden ONT transfer script's categorization of QC runs to either experiment dir or sample dir starting with "QC_".

20240422.1

Refine GHA VERSIONLOG.md check to compare to merge-base, not branch-base.

20240410.1

Expand test coverage by starting and checking demultiplexing for a NovaSeqXPlus run.

20240321.1

Include project IDs in the run folder tarball

20240315.1

Fix cases that MiSeq samplesheet misses index or index2

20240304.1

  • 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

20240229.1

Increase test coverage to 20%.

20240209.1

Implement CodeCoverage in CI.

20240208.2

Implement CI testing and increase testing coverage.

20240208.1

Fix bug with isinstance clause

20240202.1

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.

20240201.1

Fix bugs that changs in PR #404 were reverted in PR #411

20240123.1

Exclude pod5 dir and files from being copied to metadata dir.

20240122.1

Adapt ONT analysis to new ONT JSON format (also backwards compatible).

20231204.1

Update ONT instrument transfer script to ignore runs started in the 3rd PromethION column, which will be used by Clinical Genomics.

20231201.1

Run Anglerfish v0.6.0 with --lenient and --ont_barcodes options.

20231130.1

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

20231103.1

Fix bug with rsync permission issue cont.

20231031.1

Improve run_folder transfer

20231026.1

Fix bug with rsync permission issue

20231024.1

Fix functionality issues for Anglerfish launch by running via "conda run", fix erroneous file name reference and improve static typing.

20231023.1

Remove redundant cleanup_processing function in cleanup

20231016.1

Support multiple project ID for run folder transfer

20230927.1

Fix bug that NovaSeqXPlus date format cause error in writing pdc_archived timestamp

20230921.1

Remove the temp change of creating links

20230920.1

Supplement last PR, primary purpose is to differentiate user runs from QC runs in the instrument transfer script rather than the installed TACA.

20230915.1

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.

20230913.1

Fix bugs for encrypting and archiving runs on ngi-preproc cont.

20230905.1

Fix bugs for encrypting and archiving runs on ngi-preproc

20230903.1

Adapt MinKNOW .json trimming to new format from Dorado update.

20230823.1

Allow manual database update of finished ONT runs

20230822.1

Add pandas to requiresments to accomodate last PR

20230821.1

Copy ONT metadata to ngi-nas-ns.

20230814.1

Update path to store Anglerfish results.

20230810.1

Implement logging for PromethION script.

20230809.2

Update handling of MinION QC runs to not run nanoseq, only anglerfish.

20230809.1

Update PromethION script to extend the scope of the log file parsing.

20230724.1

Enable TACA to retrieve error and warnings in bcl2fastq logs

20230718.1

Update PromethION script to run rsync w. -u flag and clarify archiving code.

20230713.1

Let PromethION script search through device logs to dump flow cell pore count history into the run dir.

20230711.1

Rework how PromethION script detects runs to catch mis-named ones, too.

20230621.1

Add support for NovaSeqXPlus and improve readability

20230609.1

Add functionality to update DB of specified run dirs.

20230607.1

Trim out unused data acquisition outputs from ONT report .json files before sending them to CouchDB.

20230510.1

Add storage_systems to server_status command to allow disk space surveillance of mounted virtual NAS:es. Also added Dockerfile and devcontainer setup.

20230503.1

Change how MinKNOW reports are synced to GenStat server to increase traceability and enable transfer of the reports of finished runs.

20230502.1

Enforce MinKNOW reports retain MinKNOW run ID upon transfer to ngi-internal. Improve logging.

20230428.1

Change offload location in promethion_transfer.py

20230419.1

Use a hidden file to indicate when the final rsync of ONT data to ngi-nas is done

20230331.1

Move MinKNOW reports to ngi-internal instead of embedding in StatusDB doc

20230307.1

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

20220811.1

Set short single index to 8nt

20220614.1

Updates to promethion offload script

20220613.1

Include promethion offload script

##20220610.1 Convert statusdb urls to https

20220524.1

Handle special demux for NoIndex cases

20220520.1

Include index list from undet of complex lanes

20220427.1

Support addtional 10X index types

20220414.1

Allow 0 mismatch in demux for short single index for MiSeq

20220412.3

Bug fix and refactor handling for 10X indexes

20220412.2

Handle cases with different UMI lengths

20220412.1

Add promethion to server_status

20220409.1

Small refactor for NoIndex

20220404.1

Change cleanup irma to cleanup miarka

20220330.1

Remove "Irma" from email/log

20220328.1

Re-define signal for sequencing done

20220314.1

Refactor cleanup_nas

20220302.1

Fix bug that samplesheet of MiSeq is overwritten

20220220.1

Change samplesheet location for MiSeq

20211216.1

Add option for syncing MinION delivery data to storage

20211208.1

Updates for compability with nanoseq v2.0.1

20211201.1

Only process MinION QC runs

20211011.1

Refactor of MinION code

20211005.1

Specify CopyComplete.txt as indicator for cleaning NovaSeq runs

20210819.1

Allow 0 mismatch in demux for short single index

20210716.1

Handle special case with index 2 only for NovaSeq

20210617.1

Support addtional 10X index types

20210604.1

Handle special case with index 2 only

20210330.1

Small adjust of 10X ATACseq masks

20210323.1

Support different FC ID pattern for NextSeq2000 in bioinfo_tab.py

20210318.1

Support different FC ID pattern for NextSeq2000

20210313.1

Support addtional 10X index types

20210303.1

Fix bug that runtype was overwritten

20210302.2

Fix FC name pattern for NextSeq2000

20210302.1

Setup VERSIONLOG.md