RELEASE: staging -> master - #1943

Merged

mmorgantaylor merged 59 commits into

Sep 11, 2026

Commits on Jul 31, 2026

Compare CrosscheckMetric order- and path-insensitively

rsc3
and
claude
committed
88c7a8d
Loosen ATAC sequenced_reads threshold for nondeterminism

rsc3
and
claude
committed
33487f4
Tolerate known BWA wobble in ATAC BAM comparison

rsc3
and
claude
committed
628b186
Tolerate emptydrops nondeterminism in h5ad comparison

rsc3
and
claude
committed
a47cc2c
Use warp-tools image for h5ad compares instead of pip-installing anndata

rsc3
and
claude
committed
7e03f84
AGENTS.md: document version-bump scope (pipeline WDL vs verification/)

rsc3
and
claude
committed
300a403
Make ATAC fragment line-count tolerance relative

rsc3
and
claude
committed
eaa5394
Merge remote-tracking branch 'origin/develop' into TSPS-1082_crai_basename_qc
rsc3
committed
a8f2c89
Tolerate float variance nondeterminism in gene metrics

rsc3
and
claude
committed
237fc4d
Bump Dragmap alignment memory to fix scientific WGS OOM

rsc3
and
claude
committed
d70cd65
AGENTS.md: reflection notes (validate_release commit-first; reuse tolerant compares)

rsc3
and
claude
committed
025af44
Make GatherBamFiles non-preemptible to fix scientific WGS gather failures

rsc3
and
claude
committed
56ae79e
AGENTS.md: document preemptibility tuning for long tasks

rsc3
and
claude
committed
b412860
TSPS-1106 get rid of sample_names_map_file input (#1902)

authored
99d336e
Merge remote-tracking branch 'origin/develop' into TSPS-1082_crai_basename_qc
rsc3
committed
5ce962e
TSPS-1107 remove unused struct field (#1904)

authored
4b8614b

Commits on Aug 3, 2026

Merge branch 'develop' into TSPS-1082_crai_basename_qc
rsc3
authored
c171805
Merge pull request #1903 from broadinstitute/TSPS-1082_crai_basename_qc
rsc3
authored
b4f5e3a
Rc 3241 scanvi (#1881)

authored
2768443

Commits on Aug 4, 2026

Commits on Aug 5, 2026

Commits on Aug 6, 2026

TSPS-1108 move reheadering commands into its own task (#1905)

authored
4cc74a4
first pass at sv imputation tests
mmorgantaylor
committed
1067857
update input jsons
mmorgantaylor
committed
f043a5f
update test inputs
mmorgantaylor
committed
a3b36b5
rename inputs files to reflect what's in them
mmorgantaylor
committed
9cfeb76
Merge pull request #1909 from broadinstitute/TSPS-1039_sv_imp_warp_tests
mmorgantaylor
authored
6814f9e
add ref_dict input
mmorgantaylor
committed
58637e1
Merge pull request #1910 from broadinstitute/TSPS-1039_sv_imp_warp_tests_fix
mmorgantaylor
authored
4563b5c

Commits on Aug 7, 2026

[TSPS-1067] Update Glimpse2Ligate memory (SV pipeline) (#1911)

authored
80a48de
Lk aou mito post (#1912)
ekiernan
authored
d3ed174

Commits on Aug 11, 2026

TSPS-1045 add sample batching and removed bubble vcf output (#1916)

jsotobroad
and
Jose Soto
authored
6fa84f1

Commits on Aug 12, 2026

[TSPS-1110] Add optional INFO filter for SV Imputation pipeline (#1918)

MatthewBemis
and
actions-user
authored
2cf1d81
TSPS-1111 add in vcf manifest input option to sv imputation wdl (#1917)

authored
db2a3f1
TSPS-1116 remove all references to sv imputation concat wdl (#1920)

jsotobroad
and
Jose Soto
authored
5475cd9

Commits on Aug 13, 2026

Cleanup dead wdl (#1913)

authored
5444186
[TSPS-1113] Initial optimization of resource usage in SV Imputation tasks (#1919)

MatthewBemis
and
actions-user
authored
50aa1e1
[TSPS-1143] Add hyphen to Low-Pass WGS imputation pipeline docs (#1923)

MatthewBemis
and
actions-user
authored
88a06b7
[TSPS-1119] Remove heartbeat logic from SV Imputation (#1921)

MatthewBemis
and
actions-user
authored
27b351d

Commits on Aug 17, 2026

TSPS-1127 make all disk sizes dynamic and set bootDiskSizeGb to 0 for all tasks (#1925)

authored
21784d1

Commits on Aug 18, 2026

Commits on Aug 19, 2026

PCA website documentation (#1926)

jessicaway
and
ekiernan
authored
6f2b1d4

Commits on Aug 21, 2026

[TSPS-1147] Remove sample_ids input from SV pipeline (#1930)
salonishah11
authored
7ff89f4

Commits on Aug 25, 2026

Commits on Aug 27, 2026

Commits on Aug 28, 2026

adding updates for calculate genotype wdl (#1939)
ekiernan
authored
3568932
Lk aou phasing remove samples (#1924)
ekiernan
authored
01ef7d2

Commits on Aug 31, 2026

TSPS-1037 updates made while scale testing (#1941)

authored
abd4b28
Merge pull request #1940 from broadinstitute/develop
mmorgantaylor
authored
89b8a20

Commits on Sep 1, 2026

Commits on Sep 2, 2026

Merge pull request #1946 from broadinstitute/develop
mmorgantaylor
authored
c28d79e