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https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/README.md?plain=1#L26
This will install the `champagne` executable in pip's default location. We may want to change t…
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`/data/CCBR_Pipeliner/Exome-seek/` no longer exists for both mm10/hg38 resources.
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When connected to an interactive node from VS Code via SSH tunneling, the `$HOSTNAME` and `$SLURM_SUBMIT_HOST` environmental variables aren't set, so the host isn't detected as being biowulf in this c…
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### Description of the bug
filename pattern claims to be incorrect but the input on the design.csv file matches with the protocol guide and the fileneames was changed to match the names of the des…
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### Description of the bug
Apologies for rapid-fire bug reports. Trying to churn this analysis out before I get too busy to complete it.
The `--run_ancestry` function appears to not work on my s…
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https://github.com/CCBR/CHAMPAGNE/blob/2392eab521ce75dd818ddd74eb733a3ad5ffe6c8/nextflow.config#L56
Make this same as RENEE
`/data/CCBR_Pipeliner/SIFS` -->
https://github.com/CCBR/guis/blob/7a…
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on an interactive node, running champagne with the biowulf profile (uses slurm executor for each process)
```sh
nextflow run main.nf -profile test_mm10,biowulf -resume
```
```
ERROR ~ Error e…
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Add star fusion to the pipeline.
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### Description of the bug
When running `pgsc_calc` on a samplesheet with multiple sampleset, I get the error: `2 missing chromosomes detected! Maximum is 1. Check your samplesheet.`. Splitting the f…