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Hi!
I wanted to open a meta issue to consolidate all the efforts to actually get GATK4 to work (completely) through bioconda.
So far I've found draft PR's by
@mjsteinbaugh
@jmarshall
@ryanja…
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Hello, thanks for the plugin!
I am having some issues with it, though. It is apparently deleting intermediate files marked for use in upcoming processes. When running my pipeline (which I created m…
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### Description of the bug
As a minimal example, I am locally (on a system with 24 cores and 128 GB RAM) running joint germline with just two WES samples with this nextflow.config file
process {
…
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In the classic GATK, walkers had the option to be multi-thread in two different ways:
* `NanoSchedulable` for thread-safe `map()` calls.
* `TreeReducible` for thread-safe `map()` and `reduce()` ca…
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### Description of the bug
I get the below warning:
`WARN: A process with name 'GATK4_HAPLOTYPECALLERGVCF' is defined more than once in module script: /home/omeran/.nextflow/assets/nf-core/rnava…
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### Description of the bug
Dear All, I am facing a problem almost at the end of sarek version 3.1 for germline detection.
Could you please provide me assistance and help me to fix it?
Many Th…
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Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test
### Is your feature request related to a problem? Please describe
…
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The model endpoint files define the `filters` parameter with an examples such as:
**Existing Syntax:**
```yaml
examples:
- - variantcaller:GATK4.0
```
or
```yaml
examples:
- …
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My bwa command:
bwa-mem2 mem -M -t 24 -p -R '@RG\tID:SAMN10471711\tSM:SAMN10471711\tLB:SAMN10471711\tPL:ILLUMINA' /group/zhougrp/zhoulab/GENOMES/Chicken/EMBL/version107/GRCg7b/Gallus_gallus.bGalGal1…
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### Description of the bug
I think the problem might be the format (using .list or .bed formats) that I used to use in intervals parameter and I do not know the correct format (even after reading the…