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

nf-core

:x: *sarek/test_full_germline_ncbench_agilent* failed :crying_cat_face: *Run Name*
fabulous_poisson *Duration*
2h 6m 12s *Status*
:x: Failed *Error Message*
```(more omitted..)
I1109 23:11:57.198351 140670193836480 genomics_reader.py:223] Reading NA12878_200M.recal.cram with NativeSamReader
/tmp/Bazel.runfiles_51kcn13i/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)
I1109 23:11:57.202217 140467883991488 make_examples_core.py:3855] model.example_info filename: /opt/models/wes/model.example_info.json
I1109 23:11:57.202659 140467883991488 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wes/model.example_info.json
I1109 23:11:57.203329 140467883991488 make_examples_core.py:3876] Flags for calling:
pileup_image_height: 100
pileup_image_width: 221
I1109 23:11:57.212208 140467883991488 dv_utils.py:333] From /opt/models/wes/model.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1109 23:11:57.213102 140467883991488 make_examples_options.py:1233] Parsing AUX Fields: []
W1109 23:11:57.213689 140467883991488 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1109 23:11:57.216045 140467883991488 make_examples_core.py:384] Task 0/12: Preparing inputs
I1109 23:11:57.227874 140425672446400 genomics_reader.py:223] Reading NA12878_200M.recal.cram with NativeSamReader
/tmp/Bazel.runfiles_kfq5sifj/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)
I1109 23:11:57.248260 140498311262656 make_examples_core.py:3855] model.example_info filename: /opt/models/wes/model.example_info.json
I1109 23:11:57.248659 140498311262656 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wes/model.example...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name fabulous_poisson -params-file '<https://api.cloud.seqera.io/ephemeral/F-46MBemDsDEbPYvh45-AQ.json>' -with-tower -r dev -profile test_full_germline_ncbench_agilent``` Nov 9, 2026 at 11:12 PM