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This appears to need a better description of the formats we are willing to read:
https://github.com/r-bioinformatics/edgePy/blob/master/docs/data-formats.md
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cf https://github.com/nf-core/tools/pull/1353#pullrequestreview-831612660
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I'm dealing with PDX.
I wanted to remove ambiguous reads that map on mouse genome.
From my understanding, in the pipeline, bbsplit keep ambigous (ambiguous2=all) reads (mapped on both genome refer…
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Hi,
In your paper ([The single-cell transcriptional landscape of mammalian organogenesis](https://www.nature.com/articles/s41586-019-0969-x#Abs1)),I'm wondering how you make mouse embryos data ba…
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### Description of the bug
The test profile for the pipeline is failing to run on my HPC cluster. This does not happen with other nf-core pipelines (e.g., rnaseq). The log file (attached) is showin…
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- add cross-species alignment with 1M reads
- add ribosomal RNA contamination from RSeQC
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Hi I’m trying to run BRAKER3 an I’m doing test3.sh and I got this error
```shell
ERROR in file /srv/home/nadia/BRAKER/scripts/braker.pl at line 5473
Failed to execute: /srv/home/nadia/miniconda3…
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Hi! I am testing the pipeline on the testing set using the singularity image ctat_mutations.v3.0.1.simg. When I ran the comman I got the following error at the end of the pipeline:
```
[2021-05-25 …