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It would be prudent in general to allow access to the version report for a case through scout. If nothing else, versions of MIP, crucial references such as ExAC, OMIM, genome, gene models (i e transcr…
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**Describe the bug**
A clear and concise description of what the bug is.
I get an error message
[FATAL] 2022/07/07 06:04:07 MIP_ANALYSE - Could not find intended vcfanno_config file: TEST_REFERENC…
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> We recommend conda as the simplest framework to install PCGR and CPSR
This suggests there are other ways to do it. Could they be added to the information web page? I am using a department server …
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I annotate a VCF file with only 1-8 columns (INFO only), however, the annotated VCF has an extra "FORMAT" field in the header line.
I have tested 0.3.3, 0.3.0 and 0.2.6. The same problem happened.
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It appears that mosdepth creates *.csi index files for all bgzipped files like `per-base-coverage`. However, I cannot find those index files in the bcbio output directory. I don't find a log message t…
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Hi,
I am trying to understand the -f parameter in VarDictJava. As it states it is the allele frequency (AF). So I was wondering which population database for example GnomAD VarDict is using to get …
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The vep annotated outputs of CNVkit ends up with a huge list of annotations. For eg:
`/home/proj/long-term-stage/cancer/UMI_analysis_runs_APJ/cancer_test_datasets/panel_Tonly/cnv_tonly_wantedjay/ana…
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I put a bed file called grch38_kit_name.bed in the reference_dir but I still get "ERROR Could not find intendended '.bed file ending' for target file '' . Is there a specific naming convention I need …
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### Description of feature
When running `nf-core lint` on my pipeline it immediately fails with following error:
```
$ nf-core lint
,--./,-.
…
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## Check Documentation
I have checked the following places for your error:
- [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [x] [nf-core/raredisease pipeline d…