v2.1.5

bugfixes:

• pass through optional argument even when samplesheet not specified [#31]
• fix minimap aligner behavior with empty bam files [#32]
• allow guess_barcode to fail in demux if it is unable to guess anything [#33]
• bugfix minimap2_idxstats (erroneously attempting to index fasta) [#34]

v2.1.4

PR #30

Conda updates:

• update python 3.6 to 3.7
• update samtools 1.9 to 1.10
• add bcftools and csvkit
• cleanups and version pinning relaxation

Python updates:

• remove reports.py alignment_summary
• add read_utils.py minimap2_idxstats

v2.1.3

Bug fix in gatk and samtools version reporting.

v2.1.2

• add minimap2 aligner and add minimap2 option to read_utils.align_and_fix [#24]
• internal housekeeping: decondify Tool classes [#27]

v2.1.1

New:

• --append_run_id param added to illumina_demux

Fixed:

• JVMmemory parse fix for downsample_bams

v2.1.0

New:

• reports.py aggregate_alignment_counts command added to aggregate reports from read_utils.py bwamem_idxstats. Unlike aggregate_spike_count, it accepts a list of *.tsv files rather than requiring a directory path containing "*.spike_count.txt" files.

v2.0.21

Changed:

• memory and performance optimization of barcode counting in raw Illumina runs to better suit data from large flowcells (i.e. NovaSeq)

v2.0.20.1

fastqc threads arg fix

v2.0.20

• type fix for fastqc threads

v2.0.19

• kwarg fix for passing threads to fastqc