rnaseq-pipeline
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PavlidisLab
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
The information that the taxon provide is redundant because we already have the genome and the annotation reference identifiers. For that to work, we have to update Gemma platform identifiers...
I thought of first serializing the whole workflow with CWL, but that is definitely overkill and really challenging to achieve with our dynamic dependencies. I'm not against reusing the definitions...
- [ ] have some kind of way to specify `RSEM_DIR` to Bioluigi - [ ] make it so that CPUs and memory can be configured for preparing the reference
It would be very useful to catch process that exit with a signal and display the signal and a useful message in Luigi's task output.
The information can be retrieved from https://gemma.msl.ubc.ca/rest/v2/datasets/GSE128140 under the `batchEffect` instead of by looking at the factors tied to individual samples. Example: GSE128140
For some reason, the `TrimExperiment` task returns nothing.
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RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.