Choose primers to trim

[donkirkby]

We currently have three sets of primers that we can trim:

• HCV
• MidHCV
• SARS-CoV-2

The SARS-CoV-2 set has over 100 primers in it, so it tends to randomly match a significant number of reads. Let users specify which primers are expected in the samples, and only trim those. For the micall_watcher script, we can either upload the sample name in a text file, and let the pipeline parse the project out of it, or upload the project code in a text file.

• add project code to trimming step, and choose primer set
• create sample_info.csv file in release_test_microtest.py and pass to singularity image
• create sample_info.csv file in micall_watcher.py and upload to Kive
• choose primer set in docker driver with command-line option
• let BaseSpace user choose primer set

[donkirkby]

I think a sample_info.csv file with the sample name and project code in separate columns should work. The sample name can be displayed in reports and graphs, and the project code wouldn't need to be parsed out of the sample name. If we decide we want more details later, we can add more columns. Each sample would receive a file with one row in it.

sample	project
E1234-HIV_S1	HIV

This file would also be useful when we start collating all the result files for a run folder in the next release of Kive.

[donkirkby]

@cbrumme, we don't want the mapping stage or the BLAST search to narrow the set of references based on the project code, do we? We want to look for cross contamination from other samples, right? This task is just for narrowing the set of primers to trim.