genomics-bcftbx version 1.14.0

Various updates and fixes:

• bcftbx/JobRunner: new job runner class SlurmRunner (for Slurm-based compute clusters) PR #226
• CI testing: drop support for Python 3.6 and 3.7, add support for 3.11 and 3.12 PR #229
• bcftbx/simple_xls: fix compatibility bug with Xlsxwrtiter 3.2.2 PR #227
• bcftbx/platforms: refactor from module to a subpackage PR #220
• bcftbx/platforms: add data on sequencer run completion files PR #217
• bcftbx/IlluminaData: add 'property' method to IlluminaRun PR #217

genomics-bcftbx version 1.13.1

Patch/bugfix release:

• bcftbx/mock: bug fixed with invalid default bases mask being supplied for novaseq platform in the MockIlluminaRun class (PR #215)

genomics-bcftbx version 1.13.0

Various updates and fixes:

• bcftbx/utils: new function convert_size_to_bytes PR #213
• bcftbx/mock: MockIlluminaRun updated to add miniseq as a platform, expose flow cell mode, and create additional files (including run completion indicators) in mock run directories PR #212
• bcftbx/md5sum: reimplement md5sum function to reduce memory footprint PR #211
• bcftbx/IlluminData: fix bugs in IlluminaProject when assigning Fastqs when there is a mixture of lanes and no-lanes in Fastq names PR #210 PR #208

genomics-bcftbx version 1.12.0

Various updates and fixes:

• bcftbx/IlluminaData: add basic support for 'RunParameters.xml' files in Illumina runs PR #206
• bcftbx: add NovaSeq 6000 as a recognised sequencing platform (novaseq6000) PR #205
• bcftbx: add Python 3.9 and 3.10 to list of supported versions PR #202
• bcftbx/Pipeline: expose stderr output from the Job class PR #201
• Substantial refactoring of utility scripts (and removal of some deprecated legacy scripts):
  • utils: PR #198
  • QC-pipeline: PR #197
  • NGS-utils: PR #195
  • solid2cluster: PR #194
  • microarray: PR #192
  • build-indexes: PR #190
  • RNA-seq: PR #189
  • ChIP-seq: PR #188
  • illumina2cluster: PR #187
• bcftbx/fasta: new library module with FastaChromIterator class (relocated from split_fasta.py utility) PR #196
• bcftbx/TabFile: add TabFileIterator class (relocated from best_exons.py utility) PR #193
• bcftbx: drop support for Python 2 PR #185
• prep_sample_sheet.py: add option to reverse complement i5 indexes PR #183

genomics-bcftbx version 1.11.1

Patch/bugfix release:

• bcftbx/mock: fix mock HISEQ sample sheet data PR #181
• illumina2cluster/verify_paired.py: fix broken --version option PR #180

genomics-bcftbx version 1.11.0

Minor updates and fixes:

• bcftbx/TabFile:
  • TabFile can keep commented lines from the input file by specifying keep_commented_lines=True PR #178
  • TabFile.appendColumn method accepts new fill_value argument, to provide a default value to put into all rows in the new column PR #176
• bcftbx/mock: mock RunInfoXml updated to set the flowcell ID more consistently with real-life examples PR #177

genomics-bcftbx version 1.10.0

Minor updates and fixes including:

• bcftbx/IlluminaData:
  • relax the platform identification mechanism in IlluminaRun; Illumina-like run directories will be identified as generic illumina platform if no explicit platform is supplied or can be identified from the instrument name. Exceptions are now only raised for run directories which do not appear to come from an Illumina sequencer PR #174
  • add new properties to IlluminaRun instances: sample_sheet (SampleSheet instance) and runinfo (IlluminaRunInfo instance) PR #173
  • add new properties to IlluminaRunInfo instances: instrument, date, flowcell and lane_count (extracted from RunInfo.xml file) PR #172
  • SampleSheet class ignores trailing empty lines present in the input sample sheet file PR #171
• bcftbx/JobRunner: SimpleJobRunner reports status of join_logs in __repr__; fetch_runner handles join_logs when setting up SimpleJobRunner PR #170
• QC-pipeline: fastq_screen.sh updated to handle FastqScreen v0.13 and v0.14 PR #168

genomics-bcftbx version 1.9.1

Patch release:

• bcftbx: fix unclosed files and related bugs that were producing 'ResourceWarnings' under Python 3 tests PR #163
• bcftbx/JobRunner: improvements to thread safety of the SimpleJobRunner class when handling job completion and cleanup PR #166

genomics-bcftbx version 1.9.0

Minor updates and fixes:

• bcftbx/JobRunner: enable available number of CPUS (aka slots, cores, threads) to be set and accessed within the SimpleJobRunner and GEJobRunner classes PR #152
• bcftbx/mock: update MockIlluminaData class to enable forcing of creation of sample-level subdirectories when generating mock data PR #161
• bcftbx/IlluminaData: update SampleSheetPredictor to handle prediction of index reads, and to handle arbitrary reads PR #160
• bcftbx/htmlpagewriter: remove unused imports PR #158
• Extend the list of supported Python versions to include 3.6 and 3.8; update the licence to Academic Free License AFL 3.0 PR #157
• config/qc.setup.sample: updated to allow user-defined environment variables to take precedence over values defined in the setup file PR #156

genomics-bcftbx version 1.8.3

Patch release:

• bcftbx: remove internal version numbers from modules which still had them PR #155
• bcftbx/htmlpagewriter: update PNGBase64Encoder for Python 3 compatibility PR #154
• bcftbx/IlluminaData: SampleSheetPredictor updated to handle blank lane numbers in input samplesheet PR #153