CHANGELOG

# 1.2.7

- updates STRT-Seq to default to passing (undocumented) SC5P-R1 chemistry inputs to Cell Ranger
- 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

# 1.2.6

- updates BD Rhapsody to support v2 enhanced beads released in 2022
- resolves minor bugs in BD Rhapsody v1 

### 1.2.5.2

- updates to SLiPT-Seq subroutine to correct removing quality scores from adapter sequence
- 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

### 1.2.5.1

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

### 1.2.5

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

- 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)

### 1.2.4

- 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)  

### 1.2.3

- enables GitHub citation widget

- 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)

### 1.2.2

- 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

### 1.2.1

- bug fixes for R3 and R4 ffile inputs

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

- corrected whitelist for smartseq test job

### 1.2.0

- 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

### 1.1.7

- 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

### 1.1.6.2

- documents GUI application

- documents pre-generated references

### 1.1.6.1

- updates large files in Docker image

### 1.1.6

- 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

### 1.1.5

- add subroutine to support custom references

- update Docker build parameters

- supports application with graphical user interface

### 1.1.4

- add test data for Smart-Seq3

- update handing chemistry in set up

- correct STAR in docker container

### 1.1.3

- update paths for compatibility with Red Hat Linux (Fedora and CentOS)

- bug fixes for subroutines (SmartSeq3 processing)

- bug fixes for arithmetic operations

- updated documentation

### 1.1.2

- bug fixes for aligent parameters

- update paths to call subroutines

### 1.1.1

- 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

### 1.1.0

- 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

### 1.0.3

- unit tests for inDrops v3, SCI-Seq, Smart-Seq3

- implements support for full-length scRNA and dual indexes

- improved handling of input files and automated file detection

- automated testing with GitHub Actions

- version for submission to peer-review

### 1.0.2

- unit tests for 10x, dropseq, and icell8

- renaming tool and script

- version for public release

### 1.0.1

- improved set up call to handle restoring cloupe files for 10x

- support for index files for testing 10x

- checking for dual index files for inDrops-v3, SmartSeq3 and Sci-Seq

- adds whitelists for SmartSeq3 and MARS-Seq-2.0

### 1.0.0

- full documentation of all features

- scripts for installation

- bundle as docker with cellranger for install (w.i.p.)

- configure automated tested for GitLab or Travis CI

- support for additional technologies (16 presets)

- barcodes restored in output

- trimming script bundled

### 0.3.0

- custom whitelists for other technologies

- configure custom input technology

- test data for checking technologies (10x, DropSeq)

### 0.2.2

allow passing custom barcode whitelists (can only run in serial)

### 0.2.1

locate script directory

implement lock file to prevent multi technologies running

track last technology ran

### 0.2.0

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

### 0.1.0

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