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_3 *Duration*
8m 30s *Status*
:x: Failed *Error Message*
```(more omitted..)
I0612 08:18:44.358978 139743113667008 genomics_reader.py:223] Reading chr7_58169654-60828234.bed with NativeBedReader
I0612 08:18:44.508258 140175948767680 genomics_reader.py:223] Reading chr7_58169654-60828234.bed with NativeBedReader
Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_55v87niq/runfiles/com_google_deepvariant/deepvariant/make_examples.py", line 41, in &lt;module&gt;
    from third_party.nucleus.io.python import hts_verbose
ImportError: cannot import name 'hts_verbose' from 'third_party.nucleus.io.python' (/tmp/Bazel.runfiles_55v87niq/runfiles/com_google_deepvariant/third_party/nucleus/io/python/__init__.py)
I0612 08:18:45.025727 139743113667008 make_examples_core.py:348] Task 1/12: 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 00:00:1781252325.033598    1882 <http://sam_reader.cc:1001]|sam_reader.cc:1001]> Setting HTS_OPT_BLOCK_SIZE to 134217728
I0000 00:00:1781252325.053744    1882 <http://sam_reader.cc:1031]|sam_reader.cc:1031]> Setting CRAM reference path to 'Homo_sapiens_assembly38.fasta'
I0612 08:18:45.059151 139743113667008 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I0612 08:18:45.224554 140175948767680 make_examples_core.py:348] Task 10/12: 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 00:00:1781252325.231872    1883 <http://sam_reader.cc:1001]|sam_reader.cc:1001]> Setting HTS_OPT_BLOCK_SIZE to 134217728
I0000 00:00:1781252325.251823    1883 <http://sam_reader.cc:1031]|sam_reader.cc:1031]> Setting CRAM reference path to 'Homo_sapiens_assembly38.fasta'
I0612 08:18:45.257537 140175948767680 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I0612 08:18:45.411332 13974311...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws_3 -params-file '<https://api.cloud.seqera.io/ephemeral/xfaSSHVsd78WbhB-J8PATA.json>' -with-tower -r 375c449933215d19e26f645fd61c5bc38580e2da -profile test_full_germline_aws -resume f26ab704-e630-4ff0-96b8-1d08771c7354``` Jun 12, 2026 at 8:19 AM