v1.0.4

Substantially improves documentation, specifically the quick start and references documentation.

Full Changelog: v1.0.3...v1.0.4

v1.0.3

Tag version v1.0.3

v1.0.0

Added

• CHANGELOG.md to track changes between versions.
• Header to display pipeline info like title and name on STDOUT and in log.
• Stub commands for easier testing of pipeline logic.
• Set seed for HISAT2 build and align pseudo-random processes.
• Add splice-aware option for building HISAT2 index.

Changed

• Help message usage statement.
• Help message parameter help message display.
• Parameter specifications such as descriptions stored in parameter_specifications.json.
• Combined raw and trimmed reads FastQC steps to avoid duplication of modules and subworkflows.
• Only MultiQC reports use the unique prefix name to keep other processes from having to be repeated upon -resume.

Deprecated

Removed

Fixed

• Made capitalization of SRAlign consistent (i.e. sralign to SRAlign).
• README quick start message.
• README pipeline overview.

Security

0.3.0

Drastically simplifies testing.

0.2.0 - Alliterative Apple

Added features:

• Check contamination
• Preseq lc_extrap
• Create an overall MultiQC report for the pipeline

0.1.2: Fix errors with running out of memory after align

After alignment, using stdout qualifier generated Java heap space
error. Switched so that alignment processes write the sam file instead
of having to hold it in memory.

trev-f/sralign v0.1.0

Full Changelog: https://github.com/trev-f/sralign/commits/0.1.0