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 *Duration*
4h 48m 27s *Status*
:x: Failed *Error Message*
```(more omitted..)
  mark_flag_as_required(flag_name, flag_values)
I0812 22:55:37.157129 140493222379968 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I0812 22:55:37.157481 140493222379968 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wgs/model.example_info.json
I0812 22:55:37.157776 140493222379968 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
W0812 22:55:37.157832 140493222379968 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]
I0812 22:55:37.160737 140493222379968 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].
I0812 22:55:37.160982 140493222379968 make_examples_options.py:1233] Parsing AUX Fields: []
W0812 22:55:37.161305 140493222379968 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I0812 22:55:37.165642 140493222379968 make_examples_core.py:384] Task 10/12: Preparing inputs
/tmp/Bazel.runfiles_yv1o3zwd/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)
I0812 22:55:37.204582 139854664356288 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I0812 22:55:37.204871 139854664356288 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wgs/model.example_info.json
I0812 22:55:37.205121 13985466...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws -params-file '<https://api.cloud.seqera.io/ephemeral/-f-AHfDM1x8euy1ylUc8dg.json>' -with-tower -r 8ccac7ad37b05dd792447763bf9671b719824587 -profile test_full_germline_aws``` Aug 12, 2026 at 10:56 PM