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_2 *Duration*
4h 10m 51s *Status*
:x: Failed *Error Message*
```(more omitted..)
11:52:02.619 INFO  HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.6.2.0
11:52:02.619 INFO  HaplotypeCaller - For support and documentation go to <https://software.broadinstitute.org/gatk/>
11:52:02.619 INFO  HaplotypeCaller - Executing as root@ip-172-31-11-237.eu-west-1.compute.internal on Linux v6.1.166-197.305.amzn2023.x86_64 amd64
11:52:02.619 INFO  HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
11:52:02.620 INFO  HaplotypeCaller - Start Date/Time: August 11, 2026 at 11:52:02 AM GMT
11:52:02.620 INFO  HaplotypeCaller - ------------------------------------------------------------
11:52:02.620 INFO  HaplotypeCaller - ------------------------------------------------------------
11:52:02.620 INFO  HaplotypeCaller - HTSJDK Version: 4.2.0
11:52:02.621 INFO  HaplotypeCaller - Picard Version: 3.4.0
11:52:02.621 INFO  HaplotypeCaller - Built for Spark Version: 3.5.0
11:52:02.622 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:52:02.622 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:52:02.622 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:52:02.623 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:52:02.623 INFO  HaplotypeCaller - Deflater: IntelDeflater
11:52:02.623 INFO  HaplotypeCaller - Inflater: IntelInflater
11:52:02.623 INFO  HaplotypeCaller - GCS max retries/reopens: 20
11:52:02.623 INFO  HaplotypeCaller - Requester pays: disabled
11:52:02.623 INFO  HaplotypeCaller - Initializing engine
11:52:12.075 INFO  HaplotypeCaller - Shutting down engine
[August 11, 2026 at 11:52:12 AM GMT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=201326592
java.lang.RuntimeException: CRAM version 3.1 is not supported
	at htsjdk.samtools.cram.build.CramIO.readCramHeader(CramIO.java:132)
	at htsjdk.samtools.cram.build.CramC...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws_2 -params-file '<https://api.cloud.seqera.io/ephemeral/LhGFqQnE_6pjVDZcvDZbNg.json>' -with-tower -r 8679fe6185dc86195f9b4dbf8dce7c28de931133 -profile test_full_germline_aws -resume 2654f586-8b7b-4edf-b88e-0c272f544afb``` Aug 11, 2026 at 11:52 AM