Version 1.3.1

• Use annotation file object as input for tasks - fix #84 [5ce9bde]

Full Changelog: v1.3.0...v1.3.1

Version 1.3.0

• Reduce memory usage in RSEM quantification process [78fd890]
• Fix regression - allow usage of precomputed genome index [4a885e3]
• Minor changes to main pipeline script [a41b5dc]
• Fix issue with contig step on unstranded data [87d7db7]
• Fix file issue in fastaIndex process [36f3469]
• Update memory for mapping [e00579a]
• Fix file issues in steps for mapping and quantification indices [574a115]
• Fix syntax errors in rsem module [a7b549e]
• Refactor modules and workflows [df1731f]

Full Changelog: v1.2.1...v1.3.0

Version 1.1.5

• Reduce memory usage in RSEM quantification process

Full Changelog: v1.1.4...v1.1.5

Version 1.2.1

• Update numeric type for memory in mapping module - fix regression

Full Changelog: v1.2...v1.2.1

Version 1.2

• Add CFF file for citattion - resolve #75
• Update ci script and GH actions workflow
• Skip QC downstream steps for bams with no alignments - fix #76
• Add sample information in process tags - resolve #73
• Correct reported number of sequencing runs for non-unique ids - fix #74
• Update trace file path in main config
• DSL2 refactoring - #78 #62

Full Changelog: v1.1.4...v1.2

Version 1.1.4

• Update cross key to get bamFilesToTranscriptome and bamStatsFiles - fixes #72

Full Changelog: v1.1.3...v1.1.4

Version 1.1.3

• Handle other == NA in infer experiment script - fix #71

Full Changelog: v1.1.2...v1.1.3

Version 1.1.2

• Update numeric type for mapping memory - fixes #70

Full Changelog: v1.1.1...v1.1.2

Version 1.1.1

• Set memory limit to STAR index process - fix #66

Additional improvements and fixes:

• Update GitHub workflow
• Merge pull request #61 from guigolab/dependabot/bundler/docs/addressable-2.8.0
• Bump addressable from 2.4.0 to 2.8.0 in /docs

Full Changelog: v1.1.1...v1.1.0

Version 1.1.0

• Add output files section in readme - #58
• Change quantification process view - #59

Additional improvements and fixes:

• Switch CI to GitHub Actions
• Fix issue with sambamba repo checkout in Dockerfile

Full Changelog: v1.0.0...v1.1.0