chapmanb/bcbb — Issue #48: merging of demuxed fastq files and project-based analyses
Author: percyfal
Created: 2012-01-25 18:20:03+00:00
State: open

Hi Brad,

more of a question than an issue. I noticed you've added code (bcbio.pipeline.sample.merge_sample) to merge samples across lanes. I've been using save_diskspace=true in order to remove sam files, but this I noticed also removes the demultiplexed files, right? I just want to make sure because it affects our data delivery routines, as outlined below.

In our setup, we have situations when we run several projects on one lane, which we distinguish with an extra "description" tag in run_info, so in principle each barcode could have a description with a different project name. We then partition fastq files in a lane based on the description tag when delivering data to customers.

On a similar note, when I do analyses for customers, I've been doing it on a project-by-project basis (it makes more sense to me), and therefore written helper scripts (project_*, see https://github.com/percyfal/bcbb/tree/master/nextgen/scripts) for this purpose. project_analysis_pipeline.sh is almost a copy of automated_initial_analysis.py, but starts off with demultiplexed files. Have you had this functionality in mind (or is it even already there)?

Cheers,

Per