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Using cromwell v36, not all log output appears to be captured even if log level set to DEBUG.
For example, using the HaplotypeCallerGvcf_GATK4 reference on GitHub, if an non-existent path is provid…
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Hello there,
thank you for developing and maintaining a great pipeline!
I'm now testing a variant call option on an RNA-seq dataset. Although I have 3 replicates, for this testing I just use 1 of …
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Hi,
I got a timeout exception during cache copying on AWS S3. The cache file size is 133GB. Given the file size, more time should be allowed for cache copying. Is there any config option that can t…
XLuyu updated
3 years ago
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## Feature request
### Tool(s) involved
GATK4 launcher
### Description
Add check in the launcher to make sure the google-cloud-sdk is compatible with GATK4.
This Issue was generated from your [for…
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### Summary
In the AnalyzeCovariates documentation, there is mention of the previous GATK3 method to obtain recalibration tables before and after BQSR. There does not seem to be that functionality in…
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Hi,
I hope I'm not missing something essential - but when running gatk4 Markduplicatesspark with a conda environment using `bioconda::gatk4=4.2.3.0` (also when using the latest version) I get a USER …
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dear GATK4 helper:
does GATK4 could use the same method to GenotypingGvcfs like GATK3.7?
I have try the GATK4 GenomicsDBImport but it turns out More than one interval specified. The tool tak…
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## Bug Report
### Affected tool(s) or class(es)
_Tool/class name(s), special parameters?_
Mutect2
### Affected version(s)
- [ ] 4.1.1.0
### Description
_Describe the problem below. Provide…
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Hello, i'm trying to run GATK4 BaseRecalibratorSpark in local in a nextflow pipeline, but I got every time the same error with this command :
**gatk-launch BaseRecalibratorSpark --spark-runner LO…
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my code end ENV:
config file:
backend {
providers {
SLURM {
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
config {
files…