v2.1.0

What's Changed

• remove hardlinking and check from old release in data download script by @jharenza in #358
• update Table S1 - histologies README by @jharenza in #357
• Update to R version 4.2.3 in docker image by @ewafula in #360
• Refactoring molecular-subtyping-ATRT module by @zzgeng in #359
• remove snv consensus module "snv-callers" by @jharenza in #370
• update tmb-calculation README by @ewafula in #371
• Refactoring molecular-subtyping-CRANIO module by @zzgeng in #362
• Refactoring molecular-subtyping-EWS module by @zzgeng in #364
• Refactoring molecular-subtyping-EPN module by @zzgeng in #363
• Refactoring molecular-subtyping-chordoma module by @zzgeng in #366
• Refactoring molecular-subtyping-neurocytoma module by @zzgeng in #365
• Rerun all of the modules with the new docker image by @ewafula in #372
• Add methyl probe annotations liftover process description by @ewafula in #378
• add deconstructSigs v1.9 by @rjcorb in #377
• ⏪ make new temp module for cnv consensus with manta by @sickler-alex in #379
• Updating module per latest v12 successful run on HPC by @sangeetashukla in #381
• 🐛 Fixes bug with GNT in which the broad histology was maintained as LGG instead of GNT by @jharenza in #382
• Include data release process in the repo README by @ewafula in #376
• updated Readme by @atlas4213 in #383
• Update data release analysis process workflow scripts by @ewafula in #380
• Updated analysis: missing NBL samples in histologies file by @zzgeng in #367
• add issue template by @jharenza in #384
• update mutational signatures module by @rjcorb in #300
• Update README.md by @jharenza in #405
• Update CI subset files to include rmats by @ewafula in #406
• Clarify SNV callers included in intersect bed for WGS samples by @ewafula in #408
• Add script to download methyl files by @zzgeng in #415
• Analysis update: remove MTP section from github CI file by @zzgeng in #429
• Updated analysis: copy_number_consensus_call_manta to use only samples which do not have GATK CNV by @zzgeng in #410
• enrich cnv non-GATK samples by @zzgeng in #431
• Create CODEOWNERS by @devbyaccident in #436
• Rerun TMB calculation - test run by @AntoniaChroni in #435
• Analysis update: change LGG methylation subtyping by @zzgeng in #433
• Analysis Update: merge cnv files by @zzgeng in #419
• Analysis update: Reduce docker size by @zzgeng in #440
• Create methyl array probes annotation module by @ewafula in #411
• 👷 Change build and run analysis conditions by @devbyaccident in #445
• Updated analysis: sample 7316-4463 HGG subtyping bug by @zzgeng in #412
• Analysis update: add K28I mutation into subtyping by @zzgeng in #439
• Update analysis: Fix a typo in molecular_subtyping_HGG script by @zzgeng in #446
• Analysis update: Organize Dockerfile and reduce docker size by @zzgeng in #447
• Update focal-cn-file-preparation README by @zzgeng in #457
• Analysis Update: Add neurocytoma workflow to README by @zzgeng in #466
• Analysis Update: Add ATRT subtyping workflow to README by @zzgeng in #467
• Analysis update: Add CRANIO subtyping workflow to README by @zzgeng in #464
• Analysis update: add DMG, EGFR to methyl mol subtype by @zzgeng in #451
• Analysis Update: Add EWS subtyping workflow to README by @zzgeng in #465
• Update analysis: Update age cutoff for CRANIO, PAP by @zzgeng in #472
• Analysis update: Add workflow for HGG molecular subtyping by @zzgeng in #454
• Analysis update: Add NBL workflow to README by @zzgeng in #462
• Analysis update: Add EPN workflow to README by @zzgeng in #461
• Analysis update: Add MB workflow by @zzgeng in #460
• Add workflow to LGG README by @zzgeng in #458
• Analysis update: Add embryonal workflow to README by @zzgeng in #463
• update cancer group by @zzgeng in #453
• add PXA to molecular subtype by @zzgeng in #450
• Change the output format in molecular-subtyping-HGG module by @zzgeng in #374
• New Analysis: add Pineoblastoma subtype module by @zzgeng in #476
• add exclude path diagnosis of PB in EMB subtyping module by @jharenza in #479
• update readmes for deprecated modules, remove unused modules by @jharenza in #481
• update TP53 module/fix HGG discrepancies (2/2) by @jharenza in #478
• V12 subset enrich for samples with TP53 SV (1/2) by @jharenza in #480
• Analysis update: Incorporate the feedback of HOPE non-HGG samples for v13 by @zzgeng in #484
• (21/21) Subset v13 by @jharenza in #531
• (20/N) Independent specimens v13 by @jharenza in #530
• (19/N) Integrate/histology v13 by @jharenza in #529
• (18/N) Pathology v13 by @jharenza in #528
• (17/N) NBL v13 by @jharenza in #527
• (16/N) LGG v13 by @jharenza in #526
• (15/N) HGG v13 by @jharenza in #525
• (14/N) Pineoblastoma v13 by @jharenza in #524
• (13/N) ATRT v13 by @jharenza in #523
• (12/N) Neurocytoma v13 by @jharenza in #522
• (11/N) EWS v13 by @jharenza in #521
• (10/N) Chordoma v13 by @jharenza in #520
• (9/N) Embryonal v13 by @jharenza in #519
• (8/N) EPN v13 by @jharenza in #518
• (6-7/N) MB and CRANIO v13 by @jharenza in #517
• (5/N) TP53 v13 by @jharenza in #516
• (4-D/N) GSVA v13 by @jharenza in #515
• (4-C/N) TMB v13 by @jharenza in #514
• (4-B/N) update and run fusion summary by @jharenza in #513
• (4-A/N) Focal CN v13 by @jharenza in #512
• (3-B/N) GISTIC v13 by @jharenza in #510
• (3-A/N) Indep filt fus v13 by @jharenza in #509
• (3/N) v13 release: Run consensus CNV modules for v13 release by @zzgeng in #485
• (2/N) V13 release: pre-release QC for v13 data by @zzgeng in #473
• (1/N) v13 release: Update download script and release note by @zzgeng in #474

New Contributors

• @AntoniaChroni made their first contribution in #435

Full Changelog: v2.0.0...v2.1.0