Guillaume Poirier-Morency

There's been discussion about using a subset of [CWL](https://www.commonwl.org/) to produce a file with structured pipeline metadata. This process can be entirely automated by introspecting the Luigi task graph and...

RSEM temporary file cleanup does not always work

1

I think it might relate to NFS.

Currently, we use the SRA format for FASTQ headers which prefix the SRR run accession to the original string from the sequencer. This format is not compatible with ArrayExpress and...

In the current setup, it's possible that the AlignSample task get scheduled on a different node than the matching DownloadSample task which disrupt the NFS caching. We could first start...

This would basically resolve #13 since we would pull the information from SRA/GEO/Gemma instead of requesting it. For the local source, we would still need a flag to override a...

[RSeQC](http://rseqc.sourceforge.net/) provide a wide range of tools for that purpose.

I've relocated the logic for creating, replacing and removing raw/processed vectors in `ExpressionExperimentDao` so that all the code that manipulates vectors can benefit from removal in batch. When deleting an...