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## **Describe the bug**
The pipeline stalls or ends prematurely before the IDR steps.
I have successfully run the pipeline on datasets using the mm10 genome, but it stalls when I use custom genomes…
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Hello,
When I try to run the engine using a 40x512 network, nibble will remain on "Awaiting readyok from engine" forever.
If I try to use the engine in console mode, if I try a go command, the engi…
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- [ ] instead of pulling the latest docker images, we should use SHA, and ideally tags, to ensure the same version of the image is used
- [ ] workflows currently refer to the notebooks from "main" br…
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This is an expansion of the issue reported here: https://github.com/broadinstitute/gatk/issues/7693.
In summary we observed that when running the standard GATK warp inputs on some of our gold stand…
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## **Describe the bug**
When I start a run with this:
caper run /net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl -i /net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/6/…
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Difficulties following and understanding "chromosome by chromosome tutorial" @ https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md
1. The instructions are for running …
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Stuff that needs to be fixed within the loadout sheets:
- [x] Switch all RobertHammer pistols with their RHS variants wherever possible.
- [x] Give long range to spotter not sniper.
- [x] Snipers…
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I'm running gatk-sv workflows with AWS backend and I'm facing some issues on scatter tasks. It seems that for some of the tasks, the reconfigured-script is bad constructed. Below is an excerpt from th…
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Hi,
I am trying to create two task. MarkDuplicates followed up Samtools index of that MarkDuplicates. Both from separate dockers. The issue I think is that when samtools indexes a bam file it does…
ghost updated
3 years ago
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Now that we've updated our WDLs to 1.0, we've found that `womtool graph` no longer works. It looks like it only supports draft2 and earlier WDL.
`test.wdl`:
```
version 1.0
workflow Test { }
…