Ecosyste.ms: Issues

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GitHub / CIMAC-CIDC/cidc-schemas issues and pull requests

#582 - Bump black from 22.3.0 to 24.3.0

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#581 - add transcriptome capture v6 to rna enrichment_method

Pull Request - State: closed - Opened by crouchcd over 1 year ago - 1 comment

#580 - CIDC-1713 regenerate docs for previous

Pull Request - State: closed - Opened by scvannost over 1 year ago - 1 comment

#579 - CIDC-1713 CIDC-1714 add serum, dna qc text

Pull Request - State: closed - Opened by scvannost over 1 year ago - 1 comment

#578 - CIDC-1703 change microbiome reverse index req

Pull Request - State: closed - Opened by JamesProvencher over 1 year ago - 1 comment

#577 - remove report from atacseq

Pull Request - State: closed - Opened by crouchcd over 1 year ago - 1 comment

#576 - remove report from atacseq

Pull Request - State: closed - Opened by crouchcd almost 2 years ago - 3 comments

#575 - tcr_fastq and tcr_adaptive is_artifact value is unclear

Issue - State: closed - Opened by crouchcd almost 2 years ago - 2 comments

#574 - CIDC-1601 files, not folders

Pull Request - State: closed - Opened by scvannost almost 2 years ago - 1 comment

#573 - CIDC-1594 add urine option

Pull Request - State: closed - Opened by scvannost almost 2 years ago - 1 comment

#571 - CIDC-1571 CIDC-1572 bug fix, option; for WES

Pull Request - State: closed - Opened by scvannost almost 2 years ago - 1 comment

#570 - CIDC-1554 assert prefix codes

Pull Request - State: closed - Opened by scvannost almost 2 years ago - 1 comment

#569 - CIDC-1181 update dateparser version in order to fix PEP 495 compliance

Pull Request - State: closed - Opened by JamesProvencher almost 2 years ago - 1 comment

#568 - CIDC-1552 remove analysis from wes folder

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#567 - CIDC-1544 swap incorrect bait set for correct one

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#566 - CIDC-876 change file derivation to return None instead of erroring when not defined

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#565 - CIDC-1505 add batch column to meta.csv

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#564 - CIDC-1533 tumor-normal pairing csv update

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#563 - CIDC-1505 add TCR meta.csv generation and tests

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#562 - fix #561 account for BOM in versioned files

Pull Request - State: closed - Opened by crouchcd about 2 years ago

#560 - CIDC-1526 filepath docs, manifest tweaks

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#559 - Add prism docs

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#558 - CIDC-1519 add participant counting for csv files with unquoted strings

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#557 - CIDC-1519 Clinical patch

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#556 - CIDC-1520 patch olink metadata parser

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#555 - CIDC-1507 tweak upload folder re Len

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#554 - CIDC-1511 MIBI DM and template updates

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#553 - CIDC-1507 CIDC-1508 Update BioFX Pipeline config/ingestion files

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#552 - CIDC-1502 CIDC-1503 consolidate analysis files to assay files

Pull Request - State: closed - Opened by JamesProvencher about 2 years ago - 1 comment

#551 - CIDC-1481 add MIBI support

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#550 - CIDC-1378 handle versioned clinical CSVs

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#549 - CIDC-1278 Update docs format AND data model tweaks

Pull Request - State: closed - Opened by scvannost about 2 years ago - 1 comment

#548 - CIDC-1447 nanostring template should append as new batch

Pull Request - State: closed - Opened by scvannost about 2 years ago

#547 - CIDC-1417 Create codeql-analysis.yml

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#546 - CIDC-1385 fixes for microbiome upload

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#545 - CIDC-1421 allow jpg files for hande assay images

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#544 - CIDC-1422 add string for null values

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#543 - CIDC-1424 add filepath map for upload types

Pull Request - State: closed - Opened by scvannost over 2 years ago

#542 - Hande manifest edit

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#541 - CIDC-1382 relax H&E tumor tissue percent requirement

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago

#540 - CIDC-1410 json schema support for clinical data participant counts

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#539 - CIDC-1410 add fix for clinical data participant counting

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#538 - CIDC-1412 Add new participant alert to shipping manifest uploads

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#537 - CIDC-1388 fix oneOf

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#536 - CIDC-1393 move cnvkit to copynumber

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#535 - CIDC-1393 Remove unneeded WES analysis file, add trial_id to autogenerated

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#534 - CIDC-1393 Add automatic generation of WES analysis upload templates to email

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#533 - CIDC-1386 schemas updates for WES v3

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#532 - CIDC-1377 add bait set to wes for 10104 upload

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#531 - CIDC-987 relax new shipping req

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#530 - CIDC-987 widely relax manifest requirements

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#529 - CIDC-1351 add support for microbiome DNA, assay, and analysis

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#528 - CIDC-1355 add ctDNA assay/analysis

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#527 - CIDC-1345 Allow empty date fields in plasma manifest

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#526 - CIDC-1343 fix typo

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#525 - CIDC-1339 add long_description for pypi

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#524 - CIDC-1339 Add ctDna as assay_type to shipment manifests

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#523 - Version bumps

Pull Request - State: closed - Opened by scvannost over 2 years ago

#522 - CIDC-1303 bump for WES match update

Pull Request - State: closed - Opened by scvannost over 2 years ago - 1 comment

#521 - Wes match add

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#520 - CIDC-1303 Wes tumor-normal matching

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago - 1 comment

#519 - Regex peg

Pull Request - State: closed - Opened by scvannost over 2 years ago

#518 - CIDC-1124 update preamble reqs for mIF

Pull Request - State: closed - Opened by JamesProvencher over 2 years ago

#517 - CIDC-1218 test on python 3.8 and 9 instead of 7

Pull Request - State: closed - Opened by scvannost almost 3 years ago - 1 comment

#516 - WES 10021 Compatibility

Pull Request - State: closed - Opened by roshni-b almost 3 years ago - 1 comment

#515 - CIDC-1217 add comments to biofx analysis templates

Pull Request - State: closed - Opened by scvannost almost 3 years ago - 1 comment

#514 - WES data model updates

Pull Request - State: closed - Opened by roshni-b almost 3 years ago - 1 comment

#513 - CIDC-1194 add WES analysis pair-level comments; regen docs

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#512 - WES pipeline updates

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#511 - Fix mIF report

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment
Labels: bug

#510 - mIF: make `Imaging date` optional

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#509 - CIDC-1170 allow any non-critical CSMS-related fields to be empty

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#508 - CIDC-1178 upgrade dateparser

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment
Labels: maintenance

#507 - CIDC-1175 fix mIF excluded samples tab

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#506 - Version bump for ATACseq

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#505 - CIDC-1175 add mIF report and excluded samples tab

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#504 - Update Slide_Scanner enum

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#503 - Add `batch_id` to ATACseq assay

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#502 - Update ATAC-seq DM to receive common report file

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 2 comments

#501 - CIDC-1142 add values to WES enums to allow for S1609 TWIST

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#500 - CIDC-1130 add controls for TCRseq Adaptive template

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#499 - CIDC-1130 Add new tcr_adaptive assay; remove versioning from RNAseq

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#498 - Update Library kit enum

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 2 comments

#497 - CIDC-1126 make most TCRseq analysis files optional; flatten schema

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#496 - CIDC-1107: Update DNA Normal Blood shipping manifest

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#495 - Ops tweaks

Pull Request - State: closed - Opened by scvannost about 3 years ago - 1 comment

#494 - Add JIRA integration workflow

Pull Request - State: closed - Opened by roshni-b about 3 years ago - 1 comment

#493 - Create PR template

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#492 - Update DV200 desc

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 2 comments

#491 - Add ATACseq to assay_type enum

Pull Request - State: closed - Opened by scvannost over 3 years ago - 1 comment

#490 - Implement ATACseq analysis

Pull Request - State: closed - Opened by scvannost over 3 years ago - 1 comment

#489 - Make most numbers optional in H&E assay template

Pull Request - State: closed - Opened by scvannost over 3 years ago - 1 comment

#488 - Allow Concatenated file to be optional

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#487 - make processed_fcs CyTOF file optional

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#486 - set pypi-publish verbose flag + bump

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#485 - add example test data for CyTOF barcodes and controls

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#484 - 'Harmonized' CyTOF data model

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment

#483 - Make `Lot number` optional

Pull Request - State: closed - Opened by roshni-b over 3 years ago - 1 comment