v0.3.0

• Added simplified QC summary in .csv format (<outdir>/basic_qc_stats/basic_qc_stats.csv) (Issue #22)
• Fixed issue where SampleSheet.csv files may not parse if Instrument Type field missing from [Header] section (Issue #30)
• Added .json formatted InterOp summary, based on BaseSpace API format (<outdir>/interop_summary/interop_summary.json) (partially addresses Issue #9)

v0.2.3

• Fixed issue with the way that process.cpus was defined for the kraken2 process in nextflow.config (Issue #20)

v0.2.2

• No feature changes in this release.
• Implemented GitHub Actions-based continuous integration (CI) testing (Issue #13).

v0.2.1

• Fix issue where NextSeq SampleSheet parsing would fail when cloud-related sections were not included (Issue #15)
• Fix issue where BCLConvertData section was not included in parsed NextSeq SampleSheet output (Issue #16)

v0.2.0

• Add NextSeq support (Issue #10)

v0.1.2

Bugfixes

• Fixes issue #5, where the pipeline would fail when one or more samples had zero reads.

v0.1.1

Bugfixes

• Fix issue #3, where pipeline crashes when fewer than 5 species are detected by bracken

v0.1.0

Initial Release

Features

Performs the following analyses to gather QC information on illumina sequence data:

• Collect illumina 'interop' QC info
• FastQC for basic fastq quality scores
• Kraken & Bracken for species and genus-level taxonomic classification and contamination detection
• MultiQC to gather QC information into an interactive HTML document