v0.0.3

Highlights

Improve the efficiency of maf processing:

• Added support for user-defined MAF center lists - this offers us flexibility with running maf processing(e.g: we can specify a list of centers to re-run processing with if needed)
• Added the ability to allow us to have individual maf center processing jobs (serially) - this means we can resume maf processing at the center where it fails instead of starting over at the beginning

Converted data guide generation to Python and Quarto for easier maintenance

Technical Features

• [GEN-2152] Allow user-defined MAF center list in MAF processing step by @danlu1, @rxu17 in (#38, #41)
• [GEN-1909] Customize copy_recursive function because access requirements are now added to the data by @danlu1 (#33)
• [GEN-1833, GEN-1865] Convert data guide to Python & Quarto by @thomasyu888 in (#32)

Bug Fixes

• [GEN-1959] Ignore null cpt_genie_sample_ids during check BPC retraction step due to germline samples by @thomasyu888 in (#34)
• [GEN-2154] Add missing 19 series, correct 20 series in map by @rxu17 in (#37)
• [GEN-1614] Bump memory for consortium release process by @danlu1 in (#23)

Other

• [DPE-1253] Add PR description template by @danlu1 in (#31)
• [GEN-1473] Update staging seq_date for 16.5 aacrgenie package release by @rxu17 (#27)
• [GEN-1622] Update cfDNA part in data_guide by @danlu1 in (#24)
• Update instructions to run data guide manually by @rxu17 in (#28)
• Added UMIAMI genomic profile and oncoTree assignment strategy to data guide by @Oliversinn in (#29)

New Contributors

• @danlu1 made their first contribution in #23
• @Oliversinn made their first contribution in #29

Full Changelog: v0.0.2...v0.0.3

v0.0.2

What's Changed

• [GEN-863] Modularize patch code by splitting off patch_file function by @thomasyu888 in #22
• [GEN-1330] Setup staging pipeline by @rxu17 in #19
• [GEN-863] Add patch release by @thomasyu888 in #21

Full Changelog: v0.0.1...v0.0.2

v0.0.1

What's Changed

• [GEN-168] Add email notification for check BPC retraction step by @thomasyu888 in #1
• Add missing seq date mappings by @thomasyu888 in #2
• Update README for nf-genie by @rxu17 in #3
• [GEN-601] Update to DSL2 by @thomasyu888 in #5
• [GEN-474, GEN-500, GEN-721, GEN-379] Include data guide generation in nextflow scripts by @thomasyu888 in #4
• [GEN-786] Add VHIO-300 panel info in data guide by @thomasyu888 in #6
• Add genome nexus annotation status filter by @thomasyu888 in #7
• provide oncotree strategy by @jakevc in #8
• Update data_guide.qmd by @Chelsea-Na in #9
• Update chop.qmd by @Chelsea-Na in #10
• Update uchi genomic profile and oncotree assignment info by @Chelsea-Na in #11
• [GEN-1084] Increase memory for create_consortium_release and even out process_maf by @thomasyu888 in #12
• Update README docs by @rxu17 in #13
• [GEN-1170] Add missing profile to data guide by @rxu17 in #14
• [GEN-1157] Fix copying of data guide to BPC by @rxu17 in #15
• [GEN-1204] Use updated sage image for data guide docker by @thomasyu888 in #16
• [GEN-1196] Parameterize docker images by @rxu17 in #17
• Update to dev ghcr docker by @rxu17 in #18
• [GEN-1239] Update data guide for 16.0-public by @Chelsea-Na in #20

New Contributors

• @thomasyu888 made their first contribution in #1
• @rxu17 made their first contribution in #3
• @jakevc made their first contribution in #8
• @Chelsea-Na made their first contribution in #9

Full Changelog: https://github.com/Sage-Bionetworks-Workflows/nf-genie/commits/0.0.1