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Hello,
I am incorporating STAR-Fusion into my RNAseq pipeline and I have found that the *Chimeric read filtering parameter* `--min_pct_MM_nonspecific|M` is not recognized correclty.
```
$ /path…
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Hi,
We ran `HISAT2` (2.0.4) on a 422 sample dataset against hg19, then against hg38. Then using `featureCounts` we built some count matrices and analyzed them for differential expression and got ve…
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### Checklist
- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate
### What happened?
After creating a bunch of environments (possibly in parallel), …
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I was working on another issue and discovered that the example input YAML I was using was outdated and the workflow I was running could be run with Cromwell but not `cwltool`. Before putting out a ne…
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Should be more generalized.
With choice for read aligner:
- star
- Hisat2
choice of different assemblers (Why? Because better result: ):
* denovo:
- soap denovo trans
- Oases
- trin…
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Hi,
I used your nextflow workflow from here:
https://github.com/inab/RDConnect_RNASeq
to generate a gatk vcf file to be used as input to SmartRNASeqCaller.
The final output from running RDCo…
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I'm running some tests with tower and the `nf-core/rnaseq` pipeline and have a lot of these messages in the nextflow log - not sure whether this is a problem with tower or Nextflow and/or intended:
…
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Dear REMBRANTS team,
I have applied your pipeline to a dataset of different cell lines within the same cell type. Differential expression analysis revealed a large number of downregulated/upregulat…
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### Description of feature
Related to #2406
nf-core download could support a local repo, by performing all the functions after retrieving the repository itself i.e. zipping it up, downloading th…
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**Snakemake version**
snakemake v7.18.2
snakemake-wrapper-utils v0.5.0
**Describe the bug**
When using the TrimmomaticPE wrapper (v1.19.2; `v1.19.2/bio/trimmomatic/pe`), I noticed an issue with …