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hi, eric.
Does the version of genome and transcipts gtf affect the results when we run the pipeline, which version would be better , we use GRCh38.p14.genome.fa and gencode.v45.chr_patch_hapl_scaff.…
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### Description of the bug
I ran "nextflow run nf-core/cutandrun -profile test,conda" command after installing conda and nextflow following the instruction and got the error message
### Command used…
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Unit testing each process is great for making sure we get expected outputs during development. However, all of these unit tests really end up hampering development time when a new pipeline is forked o…
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Following our discussion with @nekrut , I am creating an issue to outline essential components for creating a barebones HIV (or other short RNA virus) genomic analysis pipeline.
Key steps for ampl…
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### Description of feature
https://www.zymoresearch.de/products/zymo-seq-switchfree-3-mrna-library-kit
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@k-florek @fanninpm @erinyoung @tives82 @DrB-S
I have been using Cecret for all things SARS-CoV-2 and our research lab just started to work up a NGS methodology for Human Norovirus sequen…
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As a bioinformatics analyst I want to generate a BED file from a gene panel for genomic test analysis so that I can use it as an input to an NGS pipeline tool.
- [ ] Get gene panel from panelapp, ref…
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### Description of feature
Hi,
Thank you for creating this awesome pipeline. I'm wondering if there are any modules within sarek that do disambiguation of mouse and human reads for PDX samples? Fo…
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Hi,
I fetched MultiQC with
```bash
curl -LOk https://github.com/ewels/MultiQC/archive/master.zip
tar -xf master.zip
cd MultiQC-master
pip install .
```
Via `where multiqc` I could also id…
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### Description of the bug
I have previously processed the GRCh38 genome with bwameth for a different pipeline that I'm trying to compare with the nf-core. So I provide the following with the input c…