0.0.6

Highlights

• Implemented staging mode for table schema updates
• Migrated to new Nextflow entry parameter

Data Processing Changes

• [GEN-2256] Added RENAL cohort data to cbio mapping table by @danlu1 in #203

Technical Features

• [GEN-1773] Implemented params.entry due to Nextflow's workflow entry option deprecation by @rxu17 in #200
• [GEN-2025] Added staging mode for table schema updates by @danlu1 in #201

Bug Fixes

• [GEN-2025] Fixed ValueError in data catalog update script by @danlu1 in #204

Other

• [GEN-2098] Melanoma pipeline config updates by @Chelsea-Na in #198
• [GEN-2214] Updated config.json by @Chelsea-Na in #205
• [GEN-2240] Updated case counts for Melanoma and Esophagogastric cohorts by @Chelsea-Na in #202

0.0.5

Highlights

• Added ability to toggle use of global response set (GRS) or cohort data dictionary for mapping
• Restructured tier1a replacement mapping tables for better maintainability
• Updated case selection logic for age limits and handling of age variables
• Implemented random selection of SDV cases based on percentage

Data Processing Changes

• [GEN-1240] Add ability to toggle GRS mapping by @rxu17 in #162
• [GEN-1744] Add tier1a replacement parameters and enable cohort specific logic by @danlu1 in #170
• [GEN-1874] Convert tier1a replacement mapping table to long format by @danlu1 in #177
• [GEN-1774] Add ability to replace with the non _DETAILED tier1a columns by @danlu1 in #178
• [GEN-1837] Add age max filter by @xindiguo in #183
• [GEN-1786] Update randomization method for SDV cases by @danlu1 in #186
• [GEN-1468] Overwrite tier1 variable by @danlu1 in #156
• [GEN-1836] Replace AGE_AT_SEQ_REPORT with AGE_AT_SEQ_REPORT_DAYS by @xindiguo in #182
• [GEN-1783] Update perform_case_selection.R age max logic by @Chelsea-Na in #187

Bug Fixes

• [GEN-1766] Fix merge_and_uncode_rca_uploads issue (missing slash) by @rxu17 in #171
• [GEN-1767] Remove the unlisting of the form column code for production fileview table by @rxu17 in #172
• [GEN-1943] Address nan in sample_id column when extracting site name by @danlu1 in #180
• [GEN-1962] Add yesno mapping to the mapping when grs is not used by @xindiguo in #181
• [GEN-1996] Fix bug with NAs in update table schema by @thomasyu888 in #189

Other

These are mainly config changes:

• [DPE-1253] Add PR description template by @danlu1 in #176
• [GEN-1727] Update config.json by @Chelsea-Na in #167
• [GEN-1756] Update config.yaml to add VICC melanoma cases by @xindiguo in #169
• [GEN-1702] Update config.json by @Chelsea-Na in #173
• [GEN-1807] Update config.yaml by @Chelsea-Na in #174
• [GEN-1889] Update config.json by @Chelsea-Na in #179
• [GEN-1986] Update config.yaml by @Chelsea-Na in #184
• [GEN-1986] Update config.yaml by @Chelsea-Na in #185
• [GEN-1786] Update randomization method by @danlu1 in #188
• [GEN-2039] Updated config for prostate 1.0-public release to use 10.3-consortium databy @Chelsea-Na in #191
• [GEN-2038] Updated config for PANC 1.0-public release to use 9.5-consortium data by @Chelsea-Na in (#192
• [GEN-2037] Updated config for BLADDER 1.0-public release to use 11.3-consortium data by @Chelsea-Na in #193
• [GEN-2044] Updated esophago cohort case target numbers due to redistribution by @Chelsea-Na in #194
• [GEN-1937] Updated configs for CRC and CRC2 cohorts to use 13.6-consortium data by @Chelsea-Na in #195
• [GEN-2089] Updated config to bundle breast and RCC cohorts using 14.6-consortium data by @Chelsea-Na in #196
• [GEN-2058] Plan to bundle breast and RCC cohorts once RCC data passes QA checks by @Chelsea-Na in #197
• [GEN-2213] Updated MELANOMA case selection target counts by @Chelsea-Na in #199

Full Changelog: 0.0.4...0.0.5

0.0.4

What's Changed

• Create dd-compare.py by @Chelsea-Na in #150
• [GEN-1478] Update config.yaml by @Chelsea-Na in #153
• [GEN-1485] Modularize update potential PHI fields by @rxu17 in #155
• Add ghcr workflow by @rxu17 in #157
• [GEN-1485] Add missing previous input to run_quac_upload_report_error step by @rxu17 in #160
• [GEN-1516, GEN-1555, GEN-1576] make table update cohort specific by @danlu1 in #158
• [GEN-1574] Add merge and decode to staging by @rxu17 in #161
• [GEN-1580] Update config.json by @Chelsea-Na in #163
• [GEN-1636] add IDs from retraction form in the retraction steps for creating clinical release files by @xindiguo in #164

Full Changelog: 0.0.3...0.0.4

0.0.3

What's Changed

• [GEN-1484] Fix mismatch between patient list in case selection and consortium release by @thomasyu888 in #146
• [GEN-1479] Add in nextflow workflow for case selection by @thomasyu888 in #145
• [GEN-1481, GEN-1488] Add validation for GENIE BPC / hardcode 17.2-consortium for export code by @thomasyu888 in #148
• [GEN-1489] Improve validation logs and remove patients from all output by @thomasyu888 in #149
• [GEN-1481] Update case selection scripts to pull from a main genie consortium release by @danlu1 in #151
• [GEN-1470] Update config.yaml(s) by @Chelsea-Na in #142
• [GEN-1503] Add nextflow workflow for clinical release by @thomasyu888 in #144
• [GEN-1476] use detailed columns to extract tier1a code by @danlu1 in #152

New Contributors

• @danlu1 made their first contribution in #151

Full Changelog: 0.0.2...0.0.3

0.0.2

What's Changed

• [GEN-1448] Fix bug that causes blank Curation and QA and Patient Characteristics tables by @rxu17 in #139
• [GEN-1456] downgrade synapseclient by @rxu17 in #140
• [GEN-1458] Refactor custom_fix function to pull from main genie release by @rxu17 in #141

Full Changelog: 0.0.1...0.0.2

0.0.1

What's Changed

• dockerfile by @hhunterzinck in #3
• update ubuntu version by @hhunterzinck in #5
• rearrange installation commands by @hhunterzinck in #7
• install python requirement directly by @hhunterzinck in #8
• another pandas install attempt by @hhunterzinck in #9
• python only from base image by @hhunterzinck in #10
• merge develop by @hhunterzinck in #12
• add scripts from processing by @hhunterzinck in #15
• experiment with Nextflow workflow by @hhunterzinck in #13
• update bpc tables with synthetic data by @hhunterzinck in #17
• read as character by @hhunterzinck in #20
• add case selection scripts by @hhunterzinck in #22
• update readmes by @hhunterzinck in #26
• stage and pass synapse config by @hhunterzinck in #28
• add script to update potential phi fields reference table by @hhunterzinck in #25
• Workflow using synthetic data and scripts by @hhunterzinck in #30
• migrate clinical file gen by @hhunterzinck in #32
• migrate bio mapping update by @hhunterzinck in #34
• update table with bpc table update tracking dates by @hhunterzinck in #36
• add table update scripts by @hhunterzinck in #38
• script to copy BPC release files to a new synapse folder by @hhunterzinck in #42
• update readme by @hhunterzinck in #49
• case selection configuration doc by @hhunterzinck in #51
• scripts for hacking patient removals form releases by @hhunterzinck in #53
• update readmes new scripts by @hhunterzinck in #55
• fix prov by @hhunterzinck in #57
• fix data frame name for radiation data by @hhunterzinck in #59
• workflow draft for processing real data by @hhunterzinck in #40
• Use SYNAPSE_AUTH_TOKEN secret by @thomasyu888 in #60
• add documentation for specifying synapse PAT by @hhunterzinck in #62
• extract sor column name from reference table by @hhunterzinck in #64
• [IBCSPRT-58] Use sagebio dockerhub images by @thomasyu888 in #68
• modify help messages and comments for clarity by @hhunterzinck in #70
• add phase 2 parameters for case selection by @hhunterzinck in #67
• add tmp retraction step by @hhunterzinck in #72
• add synapse ids of phase 2 cohorts by @hhunterzinck in #73
• [GEN-154] Update the case selection code to check postmortem seq cases by @xindiguo in #82
• Update config.yaml for CRC2 by @Chelsea-Na in #83
• GEN-586 update provenance links by @xindiguo in #85
• Cohort/site error logic mistakenly pasted from phase by @alexpaynter in #84
• remove DFCI header file for phase 2 cohorts by @xindiguo in #86
• [GEN-632] Update main.nf to include Phase 2 cohorts by @Chelsea-Na in #87
• add phase 2 cohort to nextflow config by @xindiguo in #88
• GEN-678 Add RT form back for NSCLC phase 1 by @xindiguo in #89
• [GEN-693] Update config.yaml by @Chelsea-Na in #90
• GEN-711 update production/adjusted/sdv/irr for NSCLC and CRC by @xindiguo in #91
• remove support for synapse config by @thomasyu888 in #94
• [GEN-736] Add debug mode and production parameter for bpc by @rxu17 in #96
• Add nextflow parameter validation by @rxu17 in #97
• [GEN-602] Update to dsl2 by @rxu17 in #98
• update sharedfxn to retrieve custom irr and sdv case numbers by @xindiguo in #95
• GEN-757 Add CRC phase 1 update to config file by @xindiguo in #99
• [GEN-757] MSK CRC phase 1 additional samples by @xindiguo in #100
• [GEN-710] update to retrieve phase 2 current upload count from table by @xindiguo in #101
• [GEN-793] Remove header1 in NSCLC and CRC by @xindiguo in #102
• [GEN-828] update NSCLC phase 1 production case count by @xindiguo in #103
• [GEN-904] add data2 synId to CRC2 DFCI by @Chelsea-Na in #105
• [GEN-877] remove GRS from the merge script by @xindiguo in #106
• [GEN-888] use chatgpt to convert R to Python and modify script a tiny bit by @thomasyu888 in #104
• [GEN-916] update config.yaml for updated RCC cases by @Chelsea-Na in #107
• [GEN-924] Update config.yaml by @Chelsea-Na in #108
• Revert "[GEN-924] Update config.yaml" by @Chelsea-Na in #109
• [GEN-945] Single file upload by DFCI BrCa by @xindiguo in #110
• Update config.json to add CRC2 by @xindiguo in #111
• adding crc2 to masking config.yaml by @Chelsea-Na in #112
• [GEN-970] update birth year redaction code to allow nan value by @xindiguo in #113
• Update Release Scripts by @xindiguo in #114
• look up folder children with links and download using Synapse File Link by @xindiguo in #115
• Update remove_patients_from_clinical_files.R by @xindiguo in #119
• [GEN-1152] Update to remove step by @thomasyu888 in #121
• GEN-1061 Use GRS as primary and DD as secondary mapping for merge code by @xindiguo in #122
• GEN-1179 remove custom yesno mapping by @xindiguo in #123
• [GEN-1198] Update config.yaml by @Chelsea-Na in #125
• [GEN-936] Update config.yaml by @Chelsea-Na in #127
• [GENIE-1199] use 'cohort_internal' in order to merge NSCLC and NSCLC2 by @xindiguo in #126
• [GEN-1217] Update config.yaml by @Chelsea-Na in #128
• [GEN-1260] Update config.yaml by @Chelsea-Na in #129
• [GEN-1307] Adding and updating RENAL cohort by @Chelsea-Na in #130
• Update synapseclient version and some syntax by @thomasyu888 in #131
• hotfix due to more than one table by @xindiguo in #132
• update the syntax to avoid Error 9 in GEN-1367 by @xindiguo in https://github.com/Sage-Bionet...