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*
cheeky_hilbert *Duration*
4h 33m 4s *Status*
:x: Failed *Error Message*
```(more omitted..)
I1027 13:02:43.542686 139712078967232 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.780026 140675762930112 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.780828 139750995165632 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.667888 140466498961856 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.825511 140008520438208 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.825468 140082822021568 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.825586 139848244044224 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:43.987176 139870348722624 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:44.013808 140341351125440 genomics_reader.py:223] Reading chr11_51078349-54425074.bed with NativeBedReader
I1027 13:02:44.299690 140066925334976 make_examples_core.py:384] Task 3/12: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
I1027 13:02:44.255115 139712078967232 make_examples_core.py:384] Task 5/12: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
I0000 00:00:1793106164.287693    4705 <http://sam_reader.cc:997]|sam_reader.cc:997]> Setting HTS_OPT_BLOCK_SIZE to 134217728
I1027 13:02:44.358108 140675762930112 make_examples_core.py:384] Task 6/12: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
WARNI...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name cheeky_hilbert -params-file '<https://api.cloud.seqera.io/ephemeral/yeZT20Vj2agTSOKaUVNpMg.json>' -with-tower -r 6e9b164daa2a54c98f7dda538645d340c561ac24 -profile test_full_germline_aws``` Oct 27, 2026 at 1:03 PM