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Switch GATK 3 HC/UG to GNU parallel based parallelism #301

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holtgrewe opened this issue Dec 27, 2022 · 0 comments · Fixed by #302
Closed

Switch GATK 3 HC/UG to GNU parallel based parallelism #301

holtgrewe opened this issue Dec 27, 2022 · 0 comments · Fixed by #302

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@holtgrewe
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Is your feature request related to a problem? Please describe.
The snakemake cluster parallel GATK 3 HC/UG wrappers are complex to maintain, in particular if the inner code brings its own Python.

Describe the solution you'd like
Swich to the same parallelism as applied to the GATK4 wrappers.

Describe alternatives you've considered
N/A

Additional context
N/A
@holtgrewe holtgrewe linked a pull request Dec 27, 2022 that will close this issue
feat: switch GATK 3 HC/UG to GNU parallel based multithreading (#301) #302
Merged
holtgrewe added a commit that referenced this issue Dec 28, 2022
@holtgrewe
feat: switch GATK 3 HC/UG to GNU parallel based multithreading (#301) (…
e23e300 
…#302)

* Preparing removal of cubi-conda

wip

wip

wip

wip

update readme

* wip

* wip
@tedil tedil mentioned this issue Jun 28, 2024
Merged
This was referenced Dec 9, 2024
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feat: switch GATK 3 HC/UG to GNU parallel based multithreading (#301) bihealth/snappy-pipeline
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@holtgrewe