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*
compassionate_babbage *Duration*
2h 28m 23s *Status*
:x: Failed *Error Message*
```(more omitted..)
11:28:50.330 INFO  GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.6.2.0
11:28:50.331 INFO  GetPileupSummaries - For support and documentation go to <https://software.broadinstitute.org/gatk/>
11:28:50.331 INFO  GetPileupSummaries - Executing as root@ip-172-31-6-27.eu-west-1.compute.internal on Linux v6.1.166-197.305.amzn2023.x86_64 amd64
11:28:50.331 INFO  GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v17.0.11-internal+0-adhoc..src
11:28:50.331 INFO  GetPileupSummaries - Start Date/Time: August 11, 2026 at 11:28:50 AM GMT
11:28:50.331 INFO  GetPileupSummaries - ------------------------------------------------------------
11:28:50.331 INFO  GetPileupSummaries - ------------------------------------------------------------
11:28:50.332 INFO  GetPileupSummaries - HTSJDK Version: 4.2.0
11:28:50.332 INFO  GetPileupSummaries - Picard Version: 3.4.0
11:28:50.333 INFO  GetPileupSummaries - Built for Spark Version: 3.5.0
11:28:50.335 INFO  GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:28:50.336 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:28:50.336 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:28:50.336 INFO  GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:28:50.336 INFO  GetPileupSummaries - Deflater: IntelDeflater
11:28:50.336 INFO  GetPileupSummaries - Inflater: IntelInflater
11:28:50.336 INFO  GetPileupSummaries - GCS max retries/reopens: 20
11:28:50.336 INFO  GetPileupSummaries - Requester pays: disabled
11:28:50.337 INFO  GetPileupSummaries - Initializing engine
11:28:50.854 INFO  GetPileupSummaries - Shutting down engine
[August 11, 2026 at 11:28:50 AM 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.readCramH...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name compassionate_babbage -params-file '<https://api.cloud.seqera.io/ephemeral/plvVlOfTQMY522DKlYyvyA.json>' -with-tower -r dev -profile test_full_aws``` Aug 11, 2026 at 11:29 AM