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*
5h 9m 44s *Status*
:x: Failed *Error Message*
```3:11PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
3:11PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0ae94a58f64eff1e5 instance-type=c6id.24xlarge
3:11PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
grep: write error: Broken pipe
2026-06-30 15:11:21.418363: I tensorflow/core/util/port.cc:113] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2026-06-30 15:11:21.418728: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2026-06-30 15:11:21.421456: I external/local_tsl/tsl/cuda/cudart_stub.cc:32] Could not find cuda drivers on your machine, GPU will not be used.
2026-06-30 15:11:21.456915: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
/usr/local/lib/python3.10/dist-packages/google/api_core/_python_version_support.py:275: FutureWarning: You are using a Python version (3.10.12) which Google will stop supporting in new releases of google.api_core once it reaches its end of life (2026-10-04). Please upgrade to the latest Python version, or at least Python 3.11, to continue receiving updates for google.api_core past that date.
  warnings.warn(message, FutureWarning)
2026-06-30 15:11:22.237918: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
I0630 15:11:23.174738 139751825641920 run_deepvariant.py:623] Creating a directory for intermediate results in tmp
***** Intermediate results will be written to tmp in docker. ****
I0630 15:1...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws -params-file '<https://api.cloud.seqera.io/ephemeral/XSsbUgrnPgS9G5XJe0ynxw.json>' -with-tower -r dev -profile test_full_germline_aws``` Jun 30, 2026 at 3:12 PM