Release version 2.7.0

New Features

• Added new template for accessioning bulk RNA runs without Kallisto via -p bulk_rna_no_kallisto
• Added accessioning of MadQC for unreplicated experiments if the pipeline calculated it

Release version 2.6.0

New Features

• Added template for accessioning starch files from bam input
• Added some QC values for WGBS accessioning

Bugfixes

• Added starch file accessioning for existing DNase tempalte
• Changed ChIP/ATAC derived_from for true rep IDR/overlap peak calls so that the bed files are only derived_from the bams of the two replicates being compared (i.e. ignoring any other upstream bams contributing to the pooled input peaks)

Release version 2.5.0

New Features

• Added WGBS accessioning with -p/--pipeline-type wgbs

Release version 2.4.3

Bugfixes

• Fixed a bug generating QC for single-ended ATAC bams
• Removed QC from ChIP and ATAC bigBeds

Release version 2.4.2

Bugfixes

• Fixed a DNase bug that would cause duplicate samtools QCs to be posted
• Removed QCs from DNase bigBed files

Release version 2.4.1

Bugfixes

• Various DNase tweaks to fix accessioning of SE and replicated data

Release version 2.4.0

New Features

• Metadata JSON attachments now include the corresponding experiment's accession in the filename

Bugfixes

• Tweaked DNase template

Release version 2.3.1

Bugfixes

• Added missing DNase QC metrics

Release version 2.3.0

New Features

• Added accessioning for DNase experiments (-p dnase)
• Instead of patching Experiment.analyses a separate Analysis object is now posted and linked to the experiment
• Histone ChIP and MINT-ChIP experiments now use the output type pseudo-replicated peaks instead of stable peaks

Release version 2.2.2

Note: this does not include changes made in #102, even though the bugfix below appears later in the commit history. That will be released at a later time.

Bugfixes

• Fixed a bug that limited max AWS S3 upload size to ~84 GB