This Changelog tracks changes to this project. The notes below include a summary for each release, followed by details which contain one or more of the following tags:
addedfor new features.changedfor functionality and API changes.deprecatedfor soon-to-be removed features.removedfor now removed features.fixedfor any bug fixes.securityin case of vulnerabilities.
added"Transcriptome capture v6" to rna assay templatesenrichment_method
changedallow string for DNA QC markers in normal blood/tissue and tumor tissue DNA manifestsadded"Serum" as valid processed sample type
changedremove requirement for reverse index in microbiome to allow for combined indices
fixedsamples/participants prefix for file permissioning- trailing "." means all and only direct files are used
- regardless of file extension, in case of future conversion from csv to eg xlsx
- but not any file in the "samples" or "participants" subdirectories of the trial, just in case
- use "samples/" and "participants/" for these specifically
- trailing "." means all and only direct files are used
addedurine to type of sample in manifests
changedbiofx pipeline configs for lowercase buckets and instance namesremovedATACseq analysis batch report
fixedWES pipeline error with no tumor-only samplesaddedPass at Risk option to quality of sample enum
addedassertion that non-identical file-path prefixes for upload_type must not overlap
changedupdate dateparser version in order to fix PEP 495 compliance error
removedanalysis from end of WES analysis folder in autogenerated reactions
removed'Agilent SS Human All Exon V4' bait set for wesadded'TWIST Clin Research Exome PN 104033' bait set for wes
changedderive files to return None instead of erroring when no derivation is defined
changedadded batch column to TCR meta.csv generation
changedhandling of clinical CSV files to strip any initial BOMchangedtumor-normal attempted pairing- do not return tumor samples already used in paired analysis
- flag tumor samples if already used in tumor-only analysis
- flag normal samples if already used in paired analysis and so already in biofx's Panel of Normals
- flag previously excluded tumor samples
addedMeta.csv file to TCR pipeline conifguration file
addedmilligrams to "Materials used/remaining units"changedexpanded allow empty on microbiome DNA manifestchangedupdated description used for local file paths
fixedclinical data participant counting for csv files with unquoted strings
fixedclinical data participant counting for versioned CSV filesaddedclinical data participant counting for versioned Excel files
changedMIBI DM and template, for new metadata and understandingchangedolink extra-metadata parser to be more accepting of variable fieldchangedupload folder used for making WES pipeline templates
changedpipeline configuration generated for RIMA and WESaddedingestion sheet generation for RIMAremovedmetasheet generation for RIMAaddedtumor-only sheet to tumor-normal pairing manifestremovedconfiguration/ingestion on WES assay upload
addedcurrent ctDNA and microbiome analysis files into the assay schemasremovedctDNA and microbiome analysis schemas
addedMIBI assay supportremovedunused requirement on image artifacts
addedhandling for clinical CSV files with version as first row
changedchange schemas documentation format for the portal- nested accordions with property tables
- small changes to eg titles, description, filepaths
- added back old WES templates in documentation only
- taken from commit 207330acb52f862e2b5a20c22affb3f6f1caac73
changedDM tweaks- cytof assay core: concatenation_version and normalization_version from entry to input_files
- so controls can ALSO have like samples
- misc_data: description to file_description on file
removedcollection_event_list on clinical_trialremovedcidc_participant_id and clinical on participantremovedcidc_id and aliquots on samplesremovedunused MICSSS assay
- cytof assay core: concatenation_version and normalization_version from entry to input_files
addednew lab "MSSM_MTC" to recieving party in shipping coreremovedOTU table requirement, enrichment fields from microbiome assay
addedpossibility for jpg images for hande assay data
addedpossibility for string values to some ctdna analysis columns
addedmapping from upload_type to filepath prefix
removedstrict requirement for percent tumor tissue area in hande manifest
removedstrict requirement for percent tumor tissue area in hande metadata
fixedclincal participant count in extra metadata parsing
addedalert to shipping manifests for new participantschangedexample manifest data to allow for tests of above
addednot to required for oneOf
changedmove WES analysis cnvkit to copynumber
removedWES analysis somatic/tnscope.output.mafaddedtrial id to autogenerated WES analysis upload templates
addedautomatic generate of WES analysis upload templates to email
addedwes_analysis_old and wes_tumor_only_analysis_oldaddedcompatibility with WES analysis v3 as in Len's PR (maintaining existing)changedconversions in generating analysis template automatically
added'Agilent SS Human All Exon V4' bait set option for wes assay
removedrequirement in shipping_core for assay_type
changedshipping manifests to relax lots of previously required fieldsaddedrequirement in shipping_core for manifest_id and assay_type
addedsupport for microbiome DNA, microbiome, and microbiome analysis
addedsupport for ctDNA and ctDNA analysis
addedallow empty for plasma manifest date recieved and shipped
addedctDNA as possible assay_type for manifests
changedpytest, black, click, jinja2 version bumps
addedcollection event names to WES tumor/normal automated matching CSV
addedsemi-automated tumor/normal matching for WES uploads
addedversion peg for regex library to prevent errors in date format validation
addednot provided option for mIF slide scanner modelfixedmIF template to allow empty on all nonrequired fields
addedbackwards compatibility for 10021 WES analysis