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DavidsonGroup / pears Public

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Overhauled workflow#3

Open

Shians wants to merge 80 commits intoDavidsonGroup:mainDavidsonGroup/pears:mainfrom

Shians:mainShians/pears:mainCopy head branch name to clipboard

Conversation Commits80 (80)Checks Files changed

Open

Overhauled workflow#3
Shians wants to merge 80 commits intoDavidsonGroup:mainfrom
Shians:main

Commits

Commits on Feb 4, 2026

Fixed arriba process
Shians
committed
Fixed flexiplex process
Shians
committed
Fixed fuscia process
Shians
committed
Fixed masterdata process
Shians
committed
Fixed STARsolo process
Shians
committed
Fixed main process
Shians
committed
Fix formatting in config
Shians
committed
Updated STARSolo process to use parameters
Shians
committed
Fixed deprecated uppercase Channel usage
Shians
committed
Updated gitignore
Shians
committed
Updated gitignore
Shians
committed
Changed formatFuscia to take input
Shians
committed
Added labels for resource allocation
Shians
committed
Changed output capture for runFuscia to be more specific
Shians
committed
Changed variables names to snake_case
Shians
committed
Updated param names for clarity
Shians
committed
Changed process names to camelCase
Shians
committed
Updated environment file
Shians
committed
Removed tool init script in favour of conda env file
Shians
committed
Fixed indentation
Shians
committed
Moved python script into bin
Shians
committed
Removed git submodules
Shians
committed
Moved barcodes into assets folder
Shians
committed
Moved fuscia code to bin
Shians
committed
Moved fuscia code into bin
Shians
committed
Updated processes to directly call programs without projectDir
Shians
committed

Commits on Feb 5, 2026

Restructured directories
Shians
committed
Compressed inclusion lists
Shians
committed
Added handling for gzipped inclusion list
Shians
committed
Moved download_references.sh to bin
Shians
committed
Added explicit sh call
Shians
committed
Added default environment
Shians
committed
Added parameter validation
Shians
committed
Added necessary genome and reference versions
Shians
committed
Changed R2 read length to be calculated
Shians
committed
Changed index to be compiled based on genome version param
Shians
committed
Removed arity argument
Shians
committed
Added named outputs for STARsolo process
Shians
committed
Explicit DSL2
Shians
committed
Renamed files
Shians
committed
Updated file names
Shians
committed
Restricted conda channels
Shians
committed
Updated env file versions
Shians
committed
Changed files to download as is
Shians
committed
Updated parameter defaults and documentation
Shians
committed
Update conda env creation options
Shians
committed
Updated script calls
Shians
committed

Commits on Feb 6, 2026

Changed reference download to use internal code
Shians
committed
Added options for providing existing references and index
Shians
committed
Passing reference fasta and gtf into arriba as arguments
Shians
committed
Remove redundant genome indexing process
Shians
committed
Changed mapqual to argument to pass into fuscia process
Shians
committed
Renamed masterdata to fusion_targets
Shians
committed
Changed direct params access inside processes to arguments
Shians
committed
Split formatFlexiplex and formatArriba
Shians
committed
Changed variables to snake_case
Shians
committed
Fixed genFusionTargets
Shians
committed
Fixed output name of gen_fusion_targets.py
Shians
committed

Commits on Feb 7, 2026

Added tracing and reporting by default
Shians
committed
Added trace overwrite and defaultBranch
Shians
committed
Added protocol presets
Shians
committed

Commits on Feb 8, 2026

Updated downloaded genome reference folder to use _ instead of +
Shians
committed
Updated variable syntax for consistency
Shians
committed
Changed execution permission
Shians
committed
Changed variable usage in processed to be consistent
Shians
committed
Moved output location of STAR_index
Shians
committed
Changed samtools path as it's now managed by conda
Shians
committed

Commits on Feb 9, 2026

Refactored output formatting to external python script
Shians
committed
Removed comment
Shians
committed
Added automatic generation of flexiplex arguments
Shians
committed
Fixed flexiplex pattern generation
Shians
committed

Commits on Feb 10, 2026

Changed input/output declarations for consistent syntax
Shians
committed
Removed excess comments
Shians
committed
Changed fusion caller output summary file names
Shians
committed
Updated README
Shians
committed
Updated README
Shians
committed
Updated README
Shians
committed
Fixed FUSICA link
Shians
committed
Updated resource tiers
Shians
committed
Updated README
Shians
committed

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