Fix bug with index checker EPP with preset index sets
Update index checker EPP to capture invalid bases
For AVITI manifest generation, assume idx2 > 12 cycles and no idx2 parsed means idx2 is UMI and add Ns to manifest.
Add 10X steps to comments-to-running-notes config.
Update method for fetching AVITI stats in the BCL conversion step
Fix bug with data type in frag_an_driver_gen
New EPP for parsing VC100 CSV file
Generate composite run manifests for AVITI based on index lengths.
Fix bugs with EPP in the BCL conversion step
Support AVITI protocols for lobgook and comments_to_RN
Update AVITI run stats parser to handle multiple lanes
Fix simple naming bug.
Fix bug causing MinKNOW ss generation to fail for single samples w. label.
Add logbook for PromethION and MinION.
Support both single lane and dual lane of AVITI flowcell Decide whether to include PhiX based on lane level UDF
Downprioritize column 3 of PromethION (used by CG), when running script to suggest ports.
Fix bug with zika module import cont; Change project format for AVITI run manifest
Also include Project name and sequencing setup in AVITI run manifest for PhiX
Include Project name and sequencing setup in AVITI run manifest
Ruff format
Fix bug with zika module import
Fix bug with AVITI process
Make ONT volume calculations script case-agnostic for concentration units.
When parsing Anglerfish results, upload the Anglerfish .csv dataframe to the LIMS step.
Add script for AVITI run manifest generation, re-organize repo to follow best-practice modularization and implement EPP wrapper.
Add function to fetch sample-level Q30 for AVITI
Support AVITI in the BCL conversion step
New EPP scripts for parsing AVITI run parameters and stats
Set up fixed-volume pooling by Zika for no-QC libraries.
Support Illumina DNA No-QC protocol
Improve pipreqs comparison script in CI
Fix bug to accommodate truseq single idx when writing Anglerfish samplesheet
Change pattern to run mypy for entire dir regardless of file depth.
Skip warning message for distance of special indexes
When parsing ONT sequencing libraries, use database queries to link pool samples to their respective labels.
Support VC100 in logbook
Generate Anglerfish samplesheet post database sync and name after run.
Upgrade index orientation checker to handle swapped indexes
Bugfix comparative assertion in Anglerfish parsing.
Skip special indexes for index orientation checker
For ONT samplesheet generation, accommodate kits with included barcodes.
Refactor step and UDF instrument for Amplification and Purification
Use different functions for moving MinKNOW samplesheet to ngi-nas-ns.
Update instrument logbook and running notes config to new ONT QC workflow.
Fix bug that Check Index Distance Log is not correctly attached
Fix running notes configuration for last PR.
Major ONT update and new module 'calc_from_args' for generalized calculations.
Add TAKARA_8nt_UDI and TruSeqUDv2-UDI for index checking
Close psycopg2 connections when query is done
Update the multiplication factor for total Lysate
Update GHA script to check VERSIONLOG.md diff to compare the latest PR-commit to the latest upstream/master commit instead of the commit at the base of the PR-branch.
Fix bug that seq_platform cannot be fetched when sample ID is in a wrong format
Update lane yield thresholds for NovaSeqXPlus 1.5B and 25B FC
Upgrade index checker for finlib to check index orientations
Fix bug with plate well index
Fix issue that sys stderr blocks a step to be completed
Add Genstat URL in running notes
Add lane yield threshold for NovaSeqXPlus 25B FC
Upgrade index_placement_checker to check expected index position
Enable index_distance_checker to catch case that one sample with multiple indexes
Enable index_placement_checker to verify index set
Improve warning messages for index_distance_checker
Add cDNA QC in comments_to_running_notes
New EPP for checking index placement for inhouse workset
Add lane yield threshold for NovaSeqXPlus 1.5B FC
ruff format linting
Handle special cases for Miseq samplesheet
Add PCR machine as UDF to "CytAssist Probe Release and Extension".
Add CytAssist electronic logbook.
Add PCR instrument logbook automation for Visium CytAssist protocol steps.
Add Biomek to "Selection, cDNA Synthesis and Library Construction" step.
Treat RAD-seq as regular pooling step, requested by Hamid.
In Anglerfish parsing, only try to assign barcode-specific UDFs for barcoded samples.
Handle Anglerfish result parsing for runs W/O ONT barcodes
Discover latest anglerfish run even if embedded in subdir of run dir
Enable copy_field_art2samp to copy values from Aggregate QC steps
Add CI-check to see versionlog is updated for a given pull request
Fix bug with verify index EPP
Fix bug that log is missing with index checker
Always have chemistry as amplicon for Miseq samplesheet
Fix BioAnalyzer EPP to expect row-wise samples instead of column-wise. Associated with deviation #211.
Expand 10X and SS3 indexes for MiSeq samplesheet
Fix MiSeq samplesheet generator to include options for custom primers
Enable Attaching xml files for MiSeq
Change MiSeq samplesheet to new version
Fix change in flowcell mode name that is related with control software upgrade
Re-write EPP for parsing Anglerfish results.
Fix error for RAD-seq prep pooling.
Improve logging for Zika normalization and improve docs for Zika utils func.
Implement script parse_ba_results.py.
Change Tecan instrument into UDF for logbook
Fix bug with multiple Tos breaking sendmail
Refactor UDF names for library prep amount
Remove obsoleted EPP scripts
Remove HiSeq and HiSeqX from demux EPP scripts
Add support for Illumina DNA PCR-free protocol
Update Anglerfish SS generation to accomodate 10X indices.
Change lane yield threshold for NovaSeqXPlus 10B
Change lane yield threshold for NextSeq P3
Remove special rule for no-depletion in bravo_csv
Fix parent in running notes in comments_to_running_notes
Fix couchdb conflict error with running notes
Fix bug with datatime in make_running_note_from_workset
Bugfix ONT process started runs
Replace mfs with ngi-nas-ns
Update Qubit EPP scripts to handle FLEX file format
Use the longer read for demux threshold
Fix bug that control has no project id in index checker
Enable "ONT Start Sequencing v2.0" for running notes script.
Refactor index_distance_checker
Add function to verify if sample name matches project id in index_distance_checker
Add NovaSeqXPlus in sequencing step list for readscount
Add function to verify sample name format in index_distance_checker
Accomodate Anglerfish samplesheet generation w/o any ONT barcodes.
Fix fatal error for ONT EPP by updating names of module resource.
Fix unwarranted error message when moving files to external storage by using a different shutil function. Likely issue with Python <3.8.
When calculating amounts in QC, populate both "Amount (ng)" and "Amount (fmol)", if possible. Useful for LIMSing nanopore samples.
Implement ONT and Anglerfish samplesheet generation for MinION QC.
Config updates and minor fixes from live testing the NovaSeqXPlus sequencing protocol on dummy samples on LIMS Prod.
Bugfix for deviation 173. Differentiate metadata paths for Illumina instruments.
Put generated ONT samplesheets on ngi-nas-ns instead of mfs.
Rework zika_utils.format_worklist() split transfers logic to prevent the post-split volume from ending up as less than what is allowed by the instrument.
Rename utils module to epp_utils to avoid name collision with native Python module and fix bug causing fatal error for Zika pooling.
Assign step (accidentally omitted from PR #150) to RN config.
Live troubleshooting of ONT EPPs upon deployment of new workflow to LIMS prod.
Improve modularity and readability of ONT EPP script names and contents. Also implement changes requested during live testing.
Deploy validation 23_02_zika_codebase_revamp to replace accredited codebase for pooling using Mosquito X1.
Update control lists and fetch run recipe from project for samplesheet generator
Replace formula used for ng -> molar conversion.
Improvements and bugfixes on ONT EPPs.
Add four new EPPs related to the updated ONT workflow deploying shortly.
Update after live troubleshooting of new Zika pooling code. Fix faulty variable name and improve error logging.
Support nM as a valid conc unit for Aggregate QC DNA and RNA
Differentiate Zika normalization parameters for Amplicon workflow plate set-up. Unlike QIAseq and SMARTer it should use customer metrics and a lower minimum volume.
Enable verify index and placement epp for checking wrong well format
Update 20230130.2, correct the volume and conc information that is fetched and support both nM and ng/ul pooling. General updates to make the code simpler and more maintainable.
zika_refactoring Add re-factored pooling code for Zika. Re-route to the new code ONLY for RAD-seq pooling (non-accredited). Accredited operations will run on the old code, for now.
Convert 10X dual index 2 to RC for MiSeq
Update index_checker EPP to support SMARTSEQ3 indexes
Fix issue with NaN values for fragment analyzer results
Fix bug that manual in UDF instrument is recorded in logbook
Refactor EPP scripts for qc_amount_calculation
When writing the Zika deck layout in a worklist comment, omit all commas, to prevent the line from being cut-off.
New EPP for calculating cell or nuclei conc for the new 10X Chromium workflow
Also support two new UDFs for the QIAseq miRNA and Amplicon workflows for Bravo
Large update in functionality of Zika code. Accomodate two new UDFs and enable usage in the non-validated methods SMARTer PicoRNA, QIAseq miRNA and amplicon normalization.
Refactor of the default_bravo and calc_vol functions for bravo_csv to include two new UDFs
Update amount taken and total volume for bravo_csv
Implement Zika for QIAseq setup and start refactoring Zika code into separate files zika.py and zika_methods.py
Fix bug that manual in UDF instrument is recorded in logbook
Multiple EPP changes to support the OmniC protocol v2.0
Handle special characters in PCs name
Add more optional keys for Aggregate QC
Add PromethION Sequencing in comments_to_running_notes
Fix bug with index checker with submitted container info for inhouse libraries
New EPP for copying input UDF to output
For MiSeq samplesheet, replace Experiment Name with Flowcell ID
Add new control types for samplesheet generator
Upgrade index checker to throw error for bad format indexes
Fix bug with manage_demux_stats that noindex case cannot be handled for NextSeq
Upgrade index checker for checking sample placement
Fix issue that record changes EPP cannot handle controls
Refactor index checker for better handling of smartseq indexes
Write verify indexes comments to running notes
Upgrade index checker for verifying finished library projects
Fix bug with single read MiSeq run for illumina_run_parameter_parser
Make a new logbook EPP based on Google service account
Support Biomek for logbook
Remove workset tag for CaliperGX in comments_to_running_notes
Fix path of QC_criteria.json
Update statusdb URL to use https
Fix index distance checker for cases that one sample with multiple indexes
Fix samplesheet generator for cases that one sample with multiple indexes
Rename FC and cartridge UDFs for NextSeq and add NextSeq 2000 P1
Take 2uL sample for low pipetting volume cases for the SMARTer Pico RNA workflows
Include controls in samplesheet for MiSeq, NextSeq and NovaSeq
Enable illumina_run_parameter_parser for parsing run stats for NovaSeq
Support 10X SI-TS indexes
New EPP for summarizing Aggregate QC stats into running notes, stats for QC metrics
New EPP for summarizing Aggregate QC stats into running notes
Refactor 10X index pattern names
Do not convert index 2 for finished library samples for MiSeq
New index handling method for samplesheet generator
Update illumina_run_parameter_parser for handling MiSeq run without index cycles
Multiple EPP changes to support the new OmniC protocol
Support Mosquito for logbook
Return message when no issue detected for index checker
Refactor index checker to support 10X indexes
New EPP for checking index distance
Update illumina_run_parameter_parser for parsing run stats for MiSeq
Put back Workflow for samplesheet generator for MiSeq
Replace UDF for samplesheet generator for MiSeq
Update to send email to proj coord when a running note is written from LIMS
Update samplesheet generator to handle non-QC Minion sequencing step
Remove FastQ path from MinION samplesheet
Bravo CSV EPP for new library normalization and pooling steps
EPP support for new library normalization and pooling steps
Show ERROR messages when pool volume is too high
Support selectable Fragment Analyzer for logbook
Update anglerfish results parser to support outputfile with new format
Support fmol amount calculation
Fix bug with control samples for bravo_csv
Exclude RNA no depletion protocol from volume adjustment
Update bravo_csv to support volume adjustment for high conc samples
Update threshold of max undet per lane percentage for demux step
Upgrade EPPs to support the new ONT protocol
Support additional 10X index types in samplesheet generator Update 10X index list
Support DV200 for Caliper result parser
Allow empty path for Minion QC
Fix bug with MiSeq in samplesheet generator
Better sort functions for bravo csv and samplesheet
Fix issue with error message
Add fragment analyzer protocols in comments_to_running_notes
Upgrade EPPs to support the new QIAseq miRNA protocol
Fix bug with None type comparison in copy_qubit.py
Update obtain_customer_cc.py to support custom volume
Update scripts for parsing fragment analyzer result files
Port scripts to python 3
Update illumina_run_parameter_parser for parsing run stats
Update samplesheet generator to handle blanks in sample index
Update EPP for parsing run info for NextSeq 2000, MiSeq and NovaSeq
Update EPP for parsing run info for both NextSeq 2000 and MiSeq
New EPP for parsing run info for NextSeq 2000
Support additional 10X index types in samplesheet generator Update 10X index list
Change plate name to plate id for Bravo CSV for qPCR
Add new EPP for aliquoting samples for qPCR steps
Setup VERSIONLOG.md