A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

:x: *sarek/test_full_germline_aws* failed :crying_cat_face: *Run Name*
sarek_test_full_germline_aws_3 *Duration*
40m 59s *Status*
:x: Failed *Error Message*
```(more omitted..)
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
W0811 16:45:01.446333 140297001554368 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]
I0811 16:45:01.518406 140297001554368 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].
I0811 16:45:01.518722 140297001554368 make_examples_options.py:1233] Parsing AUX Fields: []
W0811 16:45:01.519036 140297001554368 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I0811 16:45:01.588073 140297001554368 make_examples_core.py:384] Task 3/12: Preparing inputs
4:45PM ERR [seqera-fusion] Failed to load file metadata. This indicates an internal state corruption that should not occur. Check the `error` field for more details and report this issue. error="element not found" goid=643 operation=Release path=/s3/nf-core-awsmegatests/work/sarek/work-dev/test_full_germline_aws/76/a0613a08f0c7e4cd27a42744b627df/.fusion/tmp/Bazel.runfiles_4ioizchz/runfiles/com_google_deepvariant/deepvariant/labeler/__pycache__/positional_labeler.cpython-310.pyc.140345878960192
I0811 16:45:01.919741 140482628714944 make_examples_core.py:384] Task 9/12: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I0811 16:45:01.975849 140297001554368 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I0811 16:45:02.492134 140297001554368 make_examples_core.py:384] Task 3/12: Common contigs are ['chr1', 'chr2', 'chr3', '...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws_3 -params-file '<https://api.cloud.seqera.io/ephemeral/vTyEMH5FCTKsUKn1f20reA.json>' -with-tower -r codex/pin-cram-3-0 -profile test_full_germline_aws -resume 2654f586-8b7b-4edf-b88e-0c272f544afb``` Aug 11, 2026 at 4:45 PM