CHANGELOG.md

v0.1.0 (in development)

User Facing

• Add option to pull references from datahub
• Add option to send email on workflow error, with pipeline error message
• Add versions and paper references of software used to report
• Upload input bag
• Upload execution run
• Upload mRNA QC
• Create and upload output bag
• Add optional to not upload
• Update references to use bags
• Update to newer references (GRCh38.p13.v36 and GRCm38.p6.vM25)
• Use production server for data-hub reference call
• Error pipeline if submitted does not match infered
• Update execution run with "Success" or "Error"
• Error if fastq error (>2, if pe != 2, if se !=1)
• Error if pe and line count of R1 != R2
• Error if ambiguous species inference
• Remove non fastq from inputBag from the export bag config level

Background

• Remove (comment out) option to pull references from S3
• Make pull references from BioHPC default (including in biohpc.config)
• Start using new gudmaprbk dockerhub (images autobuilt)
• Moved consistency checks to be fully python
• Changed order of steps so that fastqc is done after the trim step
• Change docker images to production
• Add automated version badges
• Only calculate/report tin values on regular chromosomes (from gtf)
• Change inputBag fetch to manifest then validate (if fail fetch missing and revalidate up to 3 times)
• Retry getData and trimData processes up to once

Known Bugs

• Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production
• Override params (inputBag, fastq, species) aren't checked for integrity

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v0.0.3

User Facing