v2.4.0 - Interim module and code updates

What's Changed

• Add missing samples to tmb calculation files by @jharenza in #560
• update R and bioconductor versions by @jharenza in #568
• re-org docker file, upgrades by @jharenza in #572
• update build token/user and docker packages by @jharenza in #575
• ⚰️ Remove pull_request condition from build workflow by @devbyaccident in #576
• move analysis module action by @jharenza in #571
• Create workflow to update yaml file for manuscript by @jharenza in #578
• Module contribution counts by @jharenza in #573
• update branch to dev for contributions yaml job by @jharenza in #581
• Collect the list for packages/software version by @zzgeng in #579
• Generate plot/counts for the manuscript by @zzgeng in #580
• Manuscript: Add percentage to pie chart by @zzgeng in #583
• add compiled figure, rerun by @jharenza in #584
• Rokita/author template by @jharenza in #585
• Update manuscript: Generate tables by @zzgeng in #588
• remove gitignore til GHA works by @jharenza in #582
• MB SHH subtyping by @rjcorb in #565
• Rjcorb/569 mb shh umap by @rjcorb in #594
• rerun tables for manuscript by @jharenza in #596
• rerun author contributions for biorxiv submission - as of July 9 by @jharenza in #595
• CNV consensus w freec wxs by @jharenza in #591
• Previously missing PB subtypes added by @sangeetashukla in #601
• rerun immune-deconv with v15 by @komalsrathi in #605
• Undo cancer_group manual override for select sample_ID as per OPC_566 by @sangeetashukla in #600
• update MB SHH abridged output by @rjcorb in #602
• Manual cancer_group assigned for select sample_id with discordant pathology_diagnosis by @sangeetashukla in #610

Full Changelog: v2.3.0...v2.3.1