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## Summary
## Additional details
- QSIRecon version: unstable (8 days ago)
- Singularity version: Apptainer 1.1.7
### What were you trying to do?
Run `dsi_studio_autotrack` but skip ODF r…
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I'm using the latest Funnanotate, but when I reach the "funannotate predict" step I get this:
```
augustus: ERROR
PP::Profile: Error parsing pattern file"/sw/anaconda/2019.10/envs/funanno…
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### Description of the bug
When analyzing non-duplex reads it makes sense to set filter_min_reads to an int, however. when setting `--filter_min_reads 1` you will encounter the following error:
` --…
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Reviewer `#3` (Remarks to the Author):
In Table 6, why are the computational domains chosen as cubics for all proteins for APBS? It is unfair for APBS in terms of efficiency.
In Table 7, solvat…
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### Description of the bug
When attempting to download and install chipseq-2.0.0 with singularity containers, the 'bowtie2 align' image gives a container string parsing error. I noticed the container…
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### Description of the bug
The CellRanger index is a directory of files, and not just one. So, one should provide a directory via `--cellranger_index`; however, this throws the following error:
``…
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### Description of the bug
This issue is identical to #218, which was closed but not resolved. After debugging, the problem is that the `data` object being supplied to `DGEList(counts=data,genes=rown…
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Hi
I am trying to set up the singularity container for EarlGrey, but after building the container, I don't think there is a conda installed in the singularity container.
I built the container us…
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**Describe the bug**
There is a massive difference of computation time between Terminal CLI and the Python wrappers for `N4BiasFieldCorrection` and `DenoiseImage`
From the terminal :
N4BiasField…
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### Description of the bug
Hi,
I am trying to analyze with Sarek a few exomes with paired-end reads of 151nt, that incorporate UMIs in R1 reads. When executing fgbio CallMolecularConsensusReads fa…