universc - UniverSC Version 1.2.5.2

Full Changelog: https://github.com/minoda-lab/universc/compare/1.2.5.1...1.2.5.2

- Shell
Published by TomKellyGenetics about 2 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.6...1.2.7

- Shell
Published by TomKellyGenetics about 2 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.5.1...1.2.6

- Shell
Published by TomKellyGenetics over 2 years ago

universc - 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 (https://github.com/nf-core/modules/pull/1706)

Full Changelog: https://github.com/minoda-lab/universc/compare/1.2.4...1.2.5

- Shell
Published by TomKellyGenetics about 3 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/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 (https://github.com/nf-core/modules/pull/1706)

Release Changelog: https://github.com/minoda-lab/universc/compare/1.2.4...1.2.5

Full Changelog: https://github.com/minoda-lab/universc/compare/1.2.4...1.2.5.1

- Shell
Published by TomKellyGenetics about 3 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.3...1.2.4

- Shell
Published by TomKellyGenetics over 3 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.2...1.2.3

- Shell
Published by TomKellyGenetics over 3 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.1...1.2.2

- Shell
Published by TomKellyGenetics over 3 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.2.0...1.2.1

- Shell
Published by TomKellyGenetics about 4 years ago

universc - 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: https://github.com/minoda-lab/universc/compare/1.1.7...1.2.0

- Shell
Published by TomKellyGenetics about 4 years ago

universc - UniverSC Version 1.1.7

12 November 2021

uses reverse complement barcode whitelist for inDrops v1 and v2 (automatically generated)
updated matching to remove adapter sequence between barcodes tested locally
updates to support legacy versions (v1 and v2) of inDrops protocol
documents GUI application
documents pre-generated references
updates large files in Docker image

Full Changelog: https://github.com/minoda-lab/universc/compare/1.1.6...1.1.7

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 1.1.6

26 September 2021

update building STAR in Docker containers
updates to syntax in script and subroutines
bug fixes to allow running without --verbose parameters
minor updates to documentation for added technologies

Graphical applications (GUI-based UniverSC) are provided as binaries.

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 1.1.5

2 September, 2021

add subroutine to support custom references
update Docker build parameters
supports application with graphical user interface

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 1.1,4

30 July, 2021

add test data for Smart-Seq3
update handing chemistry in set up
correct STAR in docker container

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 1.1.3

29 June, 2021

update paths for compatibility with Red Hat Linux (Fedora and CentOS)
bug fixes for subroutines (SmartSeq3 processing)
bug fixes for arithmetic operations
updated documentation

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 1.1.2

1 June, 2021

bug fixes for aligent parameters
update paths to call subroutines

- Shell
Published by TomKellyGenetics over 4 years ago

universc - UniverSC Version 0.2.1

12 Nov, 2019

automatically locate script directory
implement lock file to prevent multi technologies running
track which last technology ran

- Shell
Published by TomKellyGenetics almost 5 years ago

universc - UniverSC Version 0.2.0

24 July, 2019

add support for SGE mode
correct passing description arguments to cellranger
separate whitelist setup for Nadia and iCELL8
configure cellranger version 3 whitelists

= add defaults

detect lane and file names
create directory for converted R1sq

- Shell
Published by TomKellyGenetics almost 5 years ago

universc - UniverSC Version 0.1.0

22 July, 2019

pass arguments to script
add set up call to configure whitelist when needed
includes a manual and version call

= detects input file

converts files if technology other than 10x

- Shell
Published by TomKellyGenetics almost 5 years ago

universc - UniverSC Version 1.1.1

20 May, 2021

update paths in documentation
bug fixes for 10x per cell data for auto chemistry
bug fixes for custom technology input without exiting setup
bug fixes for short barcode whitelist with low fraction of reads

- Shell
Published by TomKellyGenetics almost 5 years ago

universc - UniverSC Version 1.1.0

12 May, 2021

add support for new technologies:
- 5′ scRNA technologies (e.g., Smart-Seq3, ICELL8 5′ , STRT-Seq)
- full support for combinatorial indexing (e.g., BD Rhapsody, Microwell-Seq, SCI-RNA-Seq, SPLiT-Seq, SureCell/ddSEQ)
- full support for dual indexes (e.g., Fluidigm C1, ICELL8 full-length, inDrops v3, SCI-RNA-Seq, Smart-Seq3)
- non-UMI technologies (e.g., ICELL8-v2, Quartz-Seq, RamDA-Seq, Smart-Seq2, STRT-Seq)
add support for barcodes longer than 16 bp
compatilibility with counting reads for non-UMI technologies
- generates a mock UMI for non-UMI technologies
- implements an option to replace UMI with mock UMI to force counting reads only
support custom whitelists from mixed samples with a low fraction of reads
update test cases for renaming files and compressed inputs
bug fixes for computing summary statistics
addresses peer-review comments

- Shell
Published by TomKellyGenetics almost 5 years ago