John Orgera
John Orgera
### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug We are using [GATK4SPARK_APPLYBQSR](https://github.com/nf-core/modules/blob/master/modules/nf-core/gatk4/applybqsr/main.nf) in a pipeline of ours...
Addresses #1838 for the APPLYBQSR step and applies [this PR ](https://github.com/nf-core/modules/pull/7818)from the modules repo When using APPLYBQSR on an HPC with scratch enabled, the globbed *.bam copys both the input...
### Description of the bug I have written about this bug in detail in this [issue](https://github.com/nf-core/modules/issues/7792) but it has been described before. When using APPLYBQSR on an HPC with scratch...
Currently, TaskArrayCollector submits a job array only when the array reaches its configured size. In pipelines with slower task generation or variable workloads, small batches may remain in memory indefinitely...
Currently, TaskArrayCollector submits a job array only when the array reaches its configured size. In pipelines with slower task generation or variable workloads, small batches may remain in memory indefinitely...
When using MarkDuplicates on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be...
When using ADDORREPLACEREADGROUPS on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be...