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CHANGELOG
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### 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