Thanks for getting the release over the line 🫶 found a bug in deepsomatic I am fixing today. and then I'll work on fully integrating pb mutectcaller and haplotypcaller inot the GATK filtering logic.

❌ sarek/test_full_aws failed 😿 Run Name prickly_bhabha Duration 1h 59m 9s Status ❌ Failed Error Message

(more omitted..)
vsc_min_fraction_snps: 0.029
vsc_max_fraction_indels_for_non_target_sample: 0.5
vsc_max_fraction_snps_for_non_target_sample: 0.5
I1028 12:19:40.672078 139843322835392 genomics_reader.py:223] Reading HCC1395N.recal.cram with NativeSamReader
I1028 12:19:40.674623 139913965515200 genomics_reader.py:223] Reading HCC1395N.recal.cram with NativeSamReader
I1028 12:19:40.688617 139843322835392 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
I1028 12:19:40.692461 139843322835392 dv_utils.py:333] From /opt/models/deepsomatic/wes/model.example_info.json: Shape of input examples: [200, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1028 12:19:40.692775 139843322835392 make_examples_options.py:1233] Parsing AUX Fields: []
W1028 12:19:40.693220 139843322835392 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1028 12:19:40.692029 139913965515200 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
I1028 12:19:40.696034 139843322835392 make_examples_core.py:384] Task 0/12: Preparing inputs
I1028 12:19:40.695456 139913965515200 dv_utils.py:333] From /opt/models/deepsomatic/wes/model.example_info.json: Shape of input examples: [200, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1028 12:19:40.695792 139913965515200 make_examples_options.py:1233] Parsing AUX Fields: []
W1028 12:19:40.696234 139913965515200 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1028 12:19:40.698986 139913965515200 make_examples_core.py:384] Task 6/12: Preparing inputs
I1028 12:19:40.724722 139843322835392 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
I1028 12:19:40.727236 139913965515200 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
I1028 12:19:41.011229 139741974778304 make_examples_core.py:384] Task 10/12: Common cont...

Command Line

nextflow run '<https://github.com/nf-core/sarek>' -name prickly_bhabha -params-file '<https://api.cloud.seqera.io/ephemeral/6-k0WATKAoolPmXD_0NuBg.json>' -with-tower -r 6e9b164daa2a54c98f7dda538645d340c561ac24 -profile test_full_aws

Oct 28, 2026 at 12:20 PM

❌ sarek/test_full_germline_aws failed 😿 Run Name agitated_hopper Duration 4h 14m 21s Status ❌ Failed Error Message

(more omitted..)
W1028 14:35:05.554676 140328673341888 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1028 14:35:05.569393 140328673341888 make_examples_core.py:384] Task 4/12: Preparing inputs
/tmp/Bazel.runfiles_s1sfjnj5/runfiles/absl_py/absl/flags/_validators.py:233: UserWarning: Flag --mode has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
  mark_flag_as_required(flag_name, flag_values)
I1028 14:35:05.509580 139646916796864 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I1028 14:35:05.509949 139646916796864 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wgs/model.example_info.json
I1028 14:35:05.510294 139646916796864 make_examples_core.py:3876] Flags for calling:
call_small_model_examples: True
pileup_image_height: 100
pileup_image_width: 221
small_model_indel_gq_threshold: 28
small_model_snp_gq_threshold: 20
small_model_vaf_context_window_size: 51
track_ref_reads: True
trained_small_model_path: /opt/smallmodels/wgs/model.keras
W1028 14:35:05.510368 139646916796864 make_examples_core.py:3890] Flag call_small_model_examples is specified in model.example_info.json [True] but overridden by command line with value [True]
I1028 14:35:05.514524 139646916796864 dv_utils.py:333] From /opt/models/wgs/model.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1028 14:35:05.514871 139646916796864 make_examples_options.py:1233] Parsing AUX Fields: []
W1028 14:35:05.515188 139646916796864 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1028 14:35:05.517646 139646916796864 make_examples_core.py:384] Task 2/12: Preparing inputs
I1028 14:35:05.551222 139838007116224 genomics_reader.py:223] Reading NA12878.recal.cram with Nati...

Command Line

nextflow run '<https://github.com/nf-core/sarek>' -name agitated_hopper -params-file '<https://api.cloud.seqera.io/ephemeral/ZpVK3hszJ5JReEJTI79rEg.json>' -with-tower -r 6e9b164daa2a54c98f7dda538645d340c561ac24 -profile test_full_germline_aws

Oct 28, 2026 at 2:36 PM

shared a GIF

bug fix in case there are no variants in an interval. DS assigns

default

as the sample name which then breaks merging, so we need to explicitely carry it through: github.com/nf-core/sarek/pull/2347/changes Test data PR: github.com/nf-core/test-datasets/pull/2353/changes#…

some mutectcaller fixes to get the tbi and pon: https://github.com/nf-core/modules/pull/13440

Cleaning up some mutectcaller bits github.com/nf-core/sarek/pull/2348 i think then we can merge github.com/nf-core/sarek/pull/2180 nd I can fast follow a PR that fully integrates the filtering

@Maxime Garcia github.com/nf-core/sarek/pull/2277 got a blocking review from you, can you check if it's fine now, whenever you have a minute? It's not urgent

Side quest for an old tiny issue github.com/nf-core/sarek/pull/2351/changes

working on these 3 now: • this one should fix an old bug with table sorting order: github.com/nf-core/sarek/pull/2352/changes which should then pave the way for adding the filtering for parabricks and standardise with mutect2 (github.com/nf-core/sarek/pull/2349) • and then pb haplotypecaller full integration: github.com/nf-core/sarek/pull/2353 all of them are still WIP. @Famke Bäuerle I started reviewing the xengsort PR, I think there are still some blockers, but haven't add all comments yet

need a review please: https://github.com/nf-core/test-datasets/pull/2355/changes

This is ready for review now: github.com/nf-core/sarek/pull/2352 I need to regenerate almost all the snapshots in the background so this is taking a while. The core component is done and functioning

Can I pester people with some quick #C05GH685FKJ reviews? • https://github.com/nf-core/createpanelrefs/pull/103 • https://github.com/nf-core/createpanelrefs/pull/104 • https://github.com/nf-core/createpanelrefs/pull/105 • https://github.com/nf-core/createpanelrefs/pull/106

github.com/nf-core/modules/pull/13530/changes review please to support germline resources in pb

dev meetings in ~15 min?

one chunky PR to review: github.com/nf-core/sarek/pull/2349 It adds filtering to parabricks mutectcaller which required a bunch of refactoring to share the subworkflows with mutect2 (which then triggered some more refactoring to merge the two mutect2 (tumor and paired) into one)

tests are still running and snapshots updating, but since that takes a few hours I will post it for review already

quick win for docs: github.com/nf-core/sarek/pull/2357

github.com/nf-core/modules/pull/11216 another small one

github.com/nf-core/sarek/pull/2358 another small one

github.com/nf-core/sarek/pull/2345 template update

Hi, I opened github.com/nf-core/sarek/pull/2361 TMB with pyTMB on Mutect2 calls annotated with snpEff, towards github.com/nf-core/sarek/issues/495 and picking up github.com/nf-core/sarek/pull/616. It is my first sarek PR, so the CI runs need a maintainer's approval. Happy to change the approach if it should be done differently. Thanks!

I've gotten through lots of issues last week, plus we got a few new features.: github.com/nf-core/sarek/blob/…/CHANGELOG.md#… Any violent objections to me preparing a release once the last few bug fix Prs are in?

yet another pb module update: https://github.com/nf-core/modules/pull/13556/changes

not an urgent feature, but a nice to have: split out germline resources for pileupsummary vs filtering in mutect based tools: https://github.com/nf-core/sarek/pull/2367/changes

this one is ready for review: https://github.com/nf-core/sarek/pull/2363

I am going to tackle this one next github.com/nf-core/sarek/issues/1861 : MSI tool for tumor/normal calling that ideally doesn't have a restrictive commercial license. if anyone has a tool preference let me know.