A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

:x: *sarek/test_full_aws* failed :crying_cat_face: *Run Name*
sarek_test_full_aws *Duration*
2h 25m 54s *Status*
:x: Failed *Error Message*
```(more omitted..)
20:12:28.882 INFO  GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.6.2.0
20:12:28.883 INFO  GetPileupSummaries - For support and documentation go to <https://software.broadinstitute.org/gatk/>
20:12:28.883 INFO  GetPileupSummaries - Executing as root@ip-172-31-21-105.eu-west-1.compute.internal on Linux v6.1.166-197.305.amzn2023.x86_64 amd64
20:12:28.883 INFO  GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
20:12:28.883 INFO  GetPileupSummaries - Start Date/Time: July 27, 2026 at 8:12:28 PM GMT
20:12:28.883 INFO  GetPileupSummaries - ------------------------------------------------------------
20:12:28.883 INFO  GetPileupSummaries - ------------------------------------------------------------
20:12:28.884 INFO  GetPileupSummaries - HTSJDK Version: 4.2.0
20:12:28.884 INFO  GetPileupSummaries - Picard Version: 3.4.0
20:12:28.884 INFO  GetPileupSummaries - Built for Spark Version: 3.5.0
20:12:28.886 INFO  GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:12:28.886 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:12:28.886 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:12:28.886 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:12:28.886 INFO  GetPileupSummaries - Deflater: IntelDeflater
20:12:28.886 INFO  GetPileupSummaries - Inflater: IntelInflater
20:12:28.887 INFO  GetPileupSummaries - GCS max retries/reopens: 20
20:12:28.887 INFO  GetPileupSummaries - Requester pays: disabled
20:12:28.887 INFO  GetPileupSummaries - Initializing engine
20:12:29.068 INFO  GetPileupSummaries - Shutting down engine
[July 27, 2026 at 8:12:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=201326592
java.lang.RuntimeException: CRAM version 3.1 is not supported
	at htsjdk.samtools.cram.build.CramIO.readCramHeade...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_aws -params-file '<https://api.cloud.seqera.io/ephemeral/mFRplIrqMDbGN4moqF7JmQ.json>' -with-tower -r dev -profile test_full_aws``` Jul 27, 2026 at 8:12 PM