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 #133
• Fix Error 10 in GEN-1367 by @xindiguo in #134
• [GEN-1404] Update config.yaml by @Chelsea-Na in #135
• [GEN-1415] Update code to use pandas.concat by @thomasyu888 in #136
• [GEN-1424] Make sure 'None' gets read in as a string by @thomasyu888 in #138

New Contributors

• @hhunterzinck made their first contribution in #3
• @xindiguo made their first contribution in #82
• @Chelsea-Na made their first contribution in #83
• @alexpaynter made their first contribution in #84
• @rxu17 made their first contribution in #96

Full Changelog: https://github.com/Sage-Bionetworks/genie-bpc-pipeline/commits/0.0.1