v1.9.1

What's Changed

• Remove outSAMtype STAR parameter by @LKress in #13

New Contributors

• @LKress made their first contribution in #13

Full Changelog: v1.9.0...v1.9.1

v1.9.0

What's Changed

• add fastp arbitrary args via --fastp_args and add changelog by @priesgo in #12

Full Changelog: v1.8.1...v1.9.0

v1.8.1

What's Changed

• Increase submodule usability by @gipohl in #10
• Merge Gianna's work into master by @priesgo in #11
• Change Conda support in CI environment
• Add ci profile for CI purposes

New Contributors

• @gipohl made their first contribution in #10

Full Changelog: v1.8.0...v1.8.1

v1.8.0

Changes

• Add support for STAR two pass mode which increases sensitivity in novel splice junctions
• Add additional arguments for BWA mem, BWA mem 2 and STAR that enables the user to add any additional arguments

Release v1.7.0

Changes

• Add STAR for alignment of RNA-seq data
• Record software versions in the output
• Repository has been renamed from tronflow-bwa to tronflow-alignment

Release v1.6.0

Changes

• Add support for BWA mem 2

Release v1.5.1

Changes

• Amend documentation for non optional --reference
• Add tag with sample name to fastp processes
• Output BAM index created with samtools index

Release v1.5.0

Changes

• Added an initial step of read trimming with FASTP. This also provides a QC report in HTML and JSON format. To skip read trimming use --skip_trimming
• Automated tests migrated to Github
• Pipeline migrated to DSL 2
• The definition of the conda dependencies is now granular at the process level

TronFlow bwa v1.4.1

Minor changes

• Cleans up intermediate files by default

Release TronFlow BWA v1.4.0

Changes:

• Upgrade to samtools 1.12