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### Description of the bug
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /cfs/klemming/home/h/halfdan/nfc_rd/test_full/work/singularity -- Use the…
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counts_file_path must is a path to the normalized count matrix, or an in-memory AnnData object, but when you make an Anndata object, cellphonedb doesn't work!
> ------------------------------------…
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Several members of 12/15 call mentioned importance of indicating whether an assayed fusion is directly detected or inferred from an underlying assay.
Also, a need to describe the underlying rearran…
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For example, `MT-TG` is broken.
JSON
```
"ENSG00000210154": {
"biotype": [
"Mt_tRNA",
"ncRNA",
"tRNA"
],
"description": null,
"gene_sy…
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It would be nice if there was a way to convert VCFs annotated by VEP to tab format. It could be just adding the option `-tab` to `filter_vep` (and the user could just run it without filters if just …
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Hello,
When running the VEP docker for VCF annotation using customized ref genome and annotation GTF file, I keep receiving this kind of warning:
```
Use of uninitialized value $key in substitu…
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### Description of the bug
I'm running nf-core/rnaseq with the following command:
```
nextflow run nf-core/rnaseq
-r 3.14.0 …
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We noticed that isopretGUI reports slightly different numbers of differentially expressed genes, differentially spliced genes, etc. for the same input file from HBA-Delas on different machines (table …
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## Describe the issue
I want to annotate my .vcf (Called with DeepVariant) with additional AF values. There are indeed extra things added to the INFO fields (see output file example), but not the hea…