Version 0.2.1

What's Changed

• Add micromamba profile by @bonitavw in #52
• Enable running CellBender on GPU by @bonitavw in #53
• Build a single salmon index and splici for all samples by @bonitavw in #54
• Bug fix: per-cell visualizations crashed with default mt_contig and added suggestions for missing data in dashboard by @bonitavw in #55
• Separation of samtools view processes and updated kraken by @bonitavw in #56
• Added new parameter saturation_target for 10x_saturate by @bonitavw in #57
• Include alevin data in reporting dashboard by @bonitavw in #58
• Added new parameter cellbender_extraargs for CellBender by @bonitavw in #59
• Small bug fixes in kraken, geneext and generate_dashboard by @bonitavw in #60
• Automatically merges fastqs upon duplicate sampleID by @bonitavw in #61
• Added new mapping_software option "alevin_subsampled_starsolo" by @bonitavw in #62

Full Changelog: v0.2.0...v0.2.1

Version 0.2.0

What's Changed

• Added pavianCore as submodule and increased resources by @bonitavw in #41
• set limitGenomeGenerateRAM and limitBAMsortRAM as custom config variables by @bonitavw in #42
• Converted to Seqera containers & Fixed permissions by @bonitavw in #43
• MAJOR refractoring of the workflows and subworkflows & added PavianCore by @bonitavw in #44
• Added possibility of specifying kit for split-pipe by @bonitavw in #45
• Remove strict conda dependency by @bonitavw in #46
• Increase resources withLabel process_high_memory by @bonitavw in #47
• Configuration updates and improvements by @bonitavw in #48
• Major refactoring of input and emit channels and fixed env GeneExt by @bonitavw in #49
• Added html dashboard generation and reporting workflow by @bonitavw in #50
• Modify emit channels preprocs subworkflows by @bonitavw in #51

Full Changelog: v0.1.2...v0.2.0

Version 0.1.2

What's Changed

• Fix boolean expression to disable generation of BAM during STARsolo by @bonitavw in #36
• Fix STARsolo silent error because of missing pigz by @bonitavw in #37
• Fix empty MAPREADS variable by writing to file + fix seqera container by @bonitavw in #38
• Swithed to cellbender container exclusively by @bonitavw in #39
• Removed conda dependencies from geneext module by @bonitavw in #40

Full Changelog: v0.1.1...v0.1.2

Version 0.1.1

What's Changed

• docs: Add troubleshooting guide by @bonitavw in #28
• Allow disabling BAM generation via star_generateBAM config by @bonitavw in #29
• Expanded well-range support (e.g. WT kit) for parse demultiplexing by @bonitavw in #30
• Update README.md & bump manifest version by @bonitavw in #31
• Added Seqera containers to custom modules by @bonitavw in #32
• Split 10x_saturate saturation_table process into two modules by @bonitavw in #33
• Added 10x v4 to seqtech parameters by @bonitavw in #34
• Missing out specification in subworkflow by @bonitavw in #35

Full Changelog: v0.1.0...v0.1.1

Version 0.1.0

v0.1.0

Updated script to check for files instead of existing folder