CHANGELOG.md
# Changelog
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:
- `added` for new features.
- `changed` for functionality and API changes.
- `deprecated` for soon-to-be removed features.
- `removed` for now removed features.
- `fixed` for any bug fixes.
- `security` in case of vulnerabilities.
## Version `0.26.23` - 14 July 2023
- `added` "Transcriptome capture v6" to rna assay templates `enrichment_method`
## Version `0.26.22` - 27 Apr 2023
- `changed` allow string for DNA QC markers in normal blood/tissue and tumor tissue DNA manifests
- `added` "Serum" as valid processed sample type
## Version `0.26.21` - 19 Apr 2023
- `changed` remove requirement for reverse index in microbiome to allow for combined indices
## Version `0.26.20` - 04 Jan 2023
- `fixed` samples/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
## Version `0.26.19` - 27 Dec 2022
- `added` urine to type of sample in manifests
## Version `0.26.18` - 20 Dec 2022
- `changed` biofx pipeline configs for lowercase buckets and instance names
- `removed` ATACseq analysis batch report
## Version `0.26.17` - 09 Dec 2022
- `fixed` WES pipeline error with no tumor-only samples
- `added` Pass at Risk option to quality of sample enum
## Version `0.26.16` - 02 Dec 2022
- `added` assertion that non-identical file-path prefixes for upload_type must not overlap
## Version `0.26.15` - 01 Dec 2022
- `changed` update dateparser version in order to fix PEP 495 compliance error
## Version `0.26.14` - 28 Nov 2022
- `removed` analysis from end of WES analysis folder in autogenerated reactions
## Version `0.26.13` - 17 Nov 2022
- `removed` 'Agilent SS Human All Exon V4' bait set for wes
- `added` 'TWIST Clin Research Exome PN 104033' bait set for wes
## Version `0.26.12` - 10 Nov 2022
- `changed` derive files to return None instead of erroring when no derivation is defined
## Version `0.26.11` - 7 Nov 2022
- `changed` added batch column to TCR meta.csv generation
## Version `0.26.10` - 7 Nov 2022
- `changed` handling of clinical CSV files to strip any initial BOM
- `changed` tumor-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
## Version `0.26.9` - 3 Nov 2022
- `added` Meta.csv file to TCR pipeline conifguration file
## Version `0.26.8` - 31 Oct 2022
- `added` milligrams to "Materials used/remaining units"
- `changed` expanded allow empty on microbiome DNA manifest
- `changed` updated description used for local file paths
## Version `0.26.7` - 27 Oct 2022
- `fixed` clinical data participant counting for csv files with unquoted strings
## Version `0.26.6` - 27 Oct 2022
- `fixed` clinical data participant counting for versioned CSV files
- `added` clinical data participant counting for versioned Excel files
## Version `0.26.5` - 26 Oct 2022
- `changed` MIBI DM and template, for new metadata and understanding
- `changed` olink extra-metadata parser to be more accepting of variable field
- `changed` upload folder used for making WES pipeline templates
## Version `0.26.4` - 24 Oct 2022
- `changed` pipeline configuration generated for RIMA and WES
- `added` ingestion sheet generation for RIMA
- `removed` metasheet generation for RIMA
- `added` tumor-only sheet to tumor-normal pairing manifest
- `removed` configuration/ingestion on WES assay upload
## Version `0.26.3` - 20 Oct 2022
- `added` current ctDNA and microbiome analysis files into the assay schemas
- `removed` ctDNA and microbiome analysis schemas
## Version `0.26.2` - 10 Oct 2022
- `added` MIBI assay support
- `removed` unused requirement on image artifacts
## Version `0.26.1` - 7 Oct 2022
- `added` handling for clinical CSV files with version as first row
## Version `0.26.0` - 14 Sep 2022
- `changed` change 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](https://github.com/CIMAC-CIDC/cidc-schemas/tree/207330acb52f862e2b5a20c22affb3f6f1caac73)
- `changed` DM 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
- `removed` collection_event_list on clinical_trial
- `removed` cidc_participant_id and clinical on participant
- `removed` cidc_id and aliquots on samples
- `removed` unused MICSSS assay
## Version `0.25.54` - 17 Aug 2022
- `added` new lab "MSSM_MTC" to recieving party in shipping core
- `removed` OTU table requirement, enrichment fields from microbiome assay
## Version `0.25.53` - 15 Aug 2022
- `added` possibility for jpg images for hande assay data
## Version `0.25.52` - 15 Aug 2022
- `added` possibility for string values to some ctdna analysis columns
## Version `0.25.51` - 11 Aug 2022
- `added` mapping from upload_type to filepath prefix
## Version `0.25.50` - 9 Aug 2022
- `removed` strict requirement for percent tumor tissue area in hande manifest
## Version `0.25.49` - 2 Aug 2022
- `removed` strict requirement for percent tumor tissue area in hande metadata
## Version `0.25.48` - 27 Jul 2022
- `fixed` clincal participant count in extra metadata parsing
## Version `0.25.47` - 26 Jul 2022
- `added` alert to shipping manifests for new participants
- `changed` example manifest data to allow for tests of above
## Version `0.25.46` - 13 Jul 2022
- `added` not to required for oneOf
## Version `0.25.45` - 13 Jul 2022
- `changed` move WES analysis cnvkit to copynumber
## Version `0.25.44` - 13 Jul 2022
- `removed` WES analysis somatic/tnscope.output.maf
- `added` trial id to autogenerated WES analysis upload templates
## Version `0.25.43` - 12 Jul 2022
- `added` automatic generate of WES analysis upload templates to email
## Version `0.25.42` - 8 Jul 2022
- `added` wes_analysis_old and wes_tumor_only_analysis_old
- `added` compatibility with WES analysis v3 as in Len's PR (maintaining existing)
- `changed` conversions in generating analysis template automatically
## Version `0.25.41` - 17 Jun 2022
- `added` 'Agilent SS Human All Exon V4' bait set option for wes assay
## Version `0.25.40` - 13 Jun 2022
- `removed` requirement in shipping_core for assay_type
## Version `0.25.39` - 13 Jun 2022
- `changed` shipping manifests to relax lots of previously required fields
- `added` requirement in shipping_core for manifest_id and assay_type
## Version `0.25.38` - 8 Jun 2022
- `added` support for microbiome DNA, microbiome, and microbiome analysis
## Version `0.25.37` - 7 Jun 2022
- `added` support for ctDNA and ctDNA analysis
## Version `0.25.36` - 2 Jun 2022
- `added` allow empty for plasma manifest date recieved and shipped
## Version `0.25.35` - 28 Apr 2022
- `added` ctDNA as possible assay_type for manifests
## Version `0.25.34` - 28 Apr 2022
- `changed` pytest, black, click, jinja2 version bumps
## Version `0.25.33` - 21 Apr 2022
- `added` collection event names to WES tumor/normal automated matching CSV
## Version `0.25.32` - 5 Apr 2022
- `added` semi-automated tumor/normal matching for WES uploads
## Version `0.25.31` - 25 Mar 2022
- `added` version peg for regex library to prevent errors in date format validation
## Version `0.25.30` - 2 Mar 2022
- `added` not provided option for mIF slide scanner model
- `fixed` mIF template to allow empty on all nonrequired fields
## Version `0.25.29` - 27 Jan 2022
- `added` backwards compatibility for 10021 WES analysis