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### Description of the bug
Just noticed that when the pipeline is run with data from multiple libraries/runs, the pipeline produces results for each library/line separately which is a bit odd behav…
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Thanks you for developing snapATAC tools,
and i have a question:
I followed the "Integrative Analysis of PBMC scATAC-seq and scRNA-seq" pipeline.
1. drawing the prediction score in histogram…
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### Description of the bug
`rnaSPADES` step fails with the following error:
```
Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:SPADES (pooled_reads)` terminated with an error exit status (12)
....…
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# remapping
- manual annotations
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fasta files in BLAST
- [ ] back up and deprecate old fasta files i…
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# Remapping
- manual annotations
- Monica will make sure BCM annotations are in Ag Data Commons
# Change old content
- [ ] back up and deprecate old Apollo2
- [ ] back up and deprecate old fa…
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Hi,
I am running STAR fusion on a few 100s samples. All of them are 75bp PE reads.
Each sample runs on a cluster node with 8 cores, 64GB RAM without any other job running at the same time.
The tot…
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1. Create a TES task, that uses an official Nextflow docker image, OR, uses Ubuntu and downloads and installs and configures Nextflow at startup. Nextflow shall be configured to use TES as a backend…
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The RNA-Seq pipeline will stop using `factors` in its next release.
For `factorValueObjects`, it's been replaced by simply `factorValues`.
@oganm will this affect the R or Python packages?
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### Steps
- [x] Export barcodes in right format
- [x] Run [subset-bam](https://github.com/10XGenomics/subset-bam)
- [x] run VBC RNA-seq pipeline
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Hi all,
Some params are missing or needs small adjustment in the documentation:
- [ ] publish_dir > to be added in both 'Full pipeline' and 'Conversion' doc
- [ ] output > 'Name or template for t…