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*
agitated_hopper *Duration*
4h 14m 21s *Status*
:x: 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