v2.0.18

• reports.py fastqc now exposes --threads param
• docker calc_mem.py script now exposes --per-cpu param to return mem per available cpu

v2.0.17

• update Picard 2.21.1 to 2.22.2
• update novoalign 3.07.00 to 3.09.04
• expose novoalign amplicon primer trimming options in read_utils.align_and_fix
• expose bwa minimum alignment score filtering in read_utils.align_and_fix
• add file_utils.rename_fasta_sequences command

v2.0.16

New:

• allow reports.pt::fastqc to output data zip archives, as these files are used by downstream tools such as MultiQC

v2.0.15

Updated:

• update source url for obtaining gatk 3.8
  Fixes:
• allow do_not_sanitize arg to be passed to revert_bam_picard entrypoint
• ensure read_structure override works for CheckIlluminaDirectory during demux; error out if check fails
• do not discard read IDs for single-end reads after running mvicuna

v2.0.14

• Fixes and far more unit testing around zstd support
• Fixes to doc builds
• Auto-expiration of quay containers (10 weeks) for non-master branch builds

v2.0.13

Bug fixes to documentation builds as well as some updates to DEVELOPMENT_NOTES

v2.0.12

Add CLI documentation, some additional support and fixes around zstd file handling, py3 UTF decoding, etc.

v2.0.11

Add support for zstd in extract_tarball and repack_tarballs

v2.0.10

more import namespace fixing

v2.0.9

import namespace cleanup and bugfix