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

nf-core

The reason is that we are migrating from an older version of sarek to the current one.  The old version performed these analyses with Sentieon (alignment, dedup, recalibration, dnascope, dnaseq).  We need the results of both version of the pipeline to be as close as possible.

which sarek version are you migrating from?

the old version: 2.7.2 and the new one: 3.8.1

Now, I am testing the variant_calling step with just sentieon tools; but for some reason it is trying and failing to execute  NFCORE_SAREK:sarek:BAM_VARIANT_CALLING_GERMLINE_ALL:SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:CNNSCOREVARIANT.   I pulled the container manually from "<https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0>"  because it was failing to get it from <docker://nf-core/gatk:4.5.0.0>

The error is that gatk is missing this python package: gatktool

```  [May 19, 2026 at 8:32:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.02 minutes.
  Runtime.totalMemory()=167772160
  java.lang.RuntimeException: A required Python package ("gatktool") could not be imported into the Python environment. This tool requires that the GATK Python environment is properly established and activated. Please refer to GATK README.md file for instructions on setting up the GATK Python environment.
        at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.checkPythonEnvironmentForPackage(PythonScriptExecutor.java:228)
        at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.start(StreamingPythonScriptExecutor.java:121)
        at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.onTraversalStart(CNNScoreVariants.java:299)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1096)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)
  Caused by: org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException:
  python exited with 1
  Command Line: python -c import gatktool```