UniverSC Version 1.2.7

1.2.7

6 February, 2024

• updates STRT-Seq to default to passing (undocumented) SC5P-R1 chemistry inputs to Cell Ranger (resolves issues #12 and #16)
• enables SC5P-R1 chemistry to run without read2 arguments
• adds custom parameters (STRT-Seq-2018 technology) for Fan et al., (2018) https://doi.org/10.1038/s41422-018-0053-3
• adds PIP-Seq parameters for Delley et al., (2021) for V0, Clark et al., (2023) for V1 or V2, and FluentBio PIP-Seq V3 or V4
• adds VASA-Seq parameters for VASA-drop and VASA-plate

To do: feature request for Singleron GEXSCOPE v2 (CellScope), known bug in BD Rhapsody v1

Full Changelog: 1.2.6...1.2.7

UniverSC Version 1.2.6

1.2.6

25 May, 2023

• updates BD Rhapsody to support v2 enhanced beads released in 2022 (#13 #14 #15)
• resolves minor bugs in BD Rhapsody #15 1

1.2.5.2

10 March, 2023

• updates to SLiPT-Seq subroutine to correct removing quality scores from adapter sequence (#10)
• updates SLiPT-Seq barcode whitelist to allow reverse-complement in R2 and trims UMI from 8 to 10 bp
• allow mismatches to remove linker sequences for SLiPT-Seq v1 or v2.1 and allow reverse complement in R2 (for NextSeq, NovaSeq v1.5, etc)
• pass command-line arguments to configure cell ranger
• correct generating combinatorial whitelists for well-based techniques

Full Changelog: 1.2.5.1...1.2.6

UniverSC Version 1.2.5.2

Full Changelog: 1.2.5.1...1.2.5.2

UniverSC Version 1.2.5.1

18 January, 2023

1.2.5.1

• update documentation for minor version

minor patch to partially revert potentially breaking changes in v1.2.5 when running perl instead of sed

• updates PATH environment variable to call /universc/launch_universc.sh from any working directory

Patch Changelog: 1.2.5...1.2.5.1

1.2.5

• enables double or triple digit lane numbers (suppports 16 lane NovaSeq X series
  scheduled for launch in Q1 2023, expected to be compatible with older models and
  BGI or Ultima high throughput sequencing platforms)

• migrates sed calls to perl for better memory-efficiency on large input files

• set default user as "root" in docker containers and ensure that cellranger is writeable
  to allow running in nextflow or singularity (nf-core/modules#1706)

Release Changelog: 1.2.4...1.2.5

Full Changelog: 1.2.4...1.2.5.1

UniverSC Version 1.2.5

18 January, 2023

• enables double or triple digit lane numbers (suppports 16 lane NovaSeq X series
  scheduled for launch in Q1 2023, expected to be compatible with older models and
  BGI or Ultima high throughput sequencing platforms)

• migrates sed calls to perl for better memory-efficiency on large input files

• set default user as "root" in docker containers and ensure that cellranger is writeable
  to allow running in nextflow or singularity (nf-core/modules#1706)

Full Changelog: 1.2.4...1.2.5

UniverSC Version 1.2.4

17 September 2022

• enables unit testing via nextflow for nf-core module

• removes forced "auto" chemistry for 10x technology (allows setting for test fies too small for automated detection)

• sets default values for last call parameters to 10x technology if not found (allows runs without errors on 1st call)

• enables computing RNA offset parameters without warning messages (supports containerised workflows)

• resolved singularity permissions issue by running container as root user #2

Full Changelog: 1.2.3...1.2.4

UniverSC Version 1.2.3

30 May 2022

• enables GitHub citation widget (https://citation-file-format.github.io/)

• updates SmartSeq2 and SmartSeq3 default barcodes

• updates SmartSeq2 adapter sequences and documents chemistry configurations

• enables running Slurm scheduler with automatic template configuration

• correctly sets the source directory to call subroutines and whitelists on Slurm (https://stackoverflow.com/questions/56962129/how-to-get-original-location-of-script-used-for-slurm-job)

Full Changelog: 1.2.2...1.2.3

UniverSC Version 1.2.2

23 May 2022

• bug fixes for detecting I1 and I2 files

• updates smartseq2 parameters for optional full-length or 5' end alignment (non-UMI read counts)

• document full-length chemistry parameters

Full Changelog: 1.2.1...1.2.2

UniverSC Version 1.2.1

14 February 2022

• bug fixes for R3 and R4 ffile inputs

• bug fixes for compressed fastq.gz in I1 and I2

• corrected whitelist for smartseq test job

Full Changelog: 1.2.0...1.2.1

UniverSC Version 1.2.0

26 January 2022

• backend to fully functional GUI app

• updates to support 10x 3` scRNA version 1

• updates test jobs and test data for SmartSeq3

• automated file detection for R3 and R4 read files

Full Changelog: 1.1.7...1.2.0