-
Notifications
You must be signed in to change notification settings - Fork 4
Description
Some places in the SPP still identify blanks by looking for the string "BLANK" at the beginning of the sample name, which is is inconsistent with how it is being done in kl-metapool for modern sample sheets (which use the SampleContext section) and is going to break if we try to implement katharoseq (or any other kind of non-extraction) blanks.
I've managed to get rid of most of the ones that are in the shotgun processing, but a couple remain because they are in code that is shared between both amplicon and shotgun. I haven't dealt with ANY of the ones in amplicon-specific processing.
The shared ones I know about are in Assay._replace_tube_ids_w_sample_names
:
qp-knight-lab-processing/src/qp_klp/Assays.py
Lines 56 to 58 in 2b7832e
sample_name = df.at[i, "sample_name"] | |
# blanks do not get their names swapped. | |
if sample_name.startswith('BLANK'): |
... and in Workflow._compare_samples_against_qiita
:
qp-knight-lab-processing/src/qp_klp/Workflows.py
Lines 497 to 500 in 2b7832e
# do not include BLANKs. If they are unregistered, we will add | |
# them downstream. | |
samples = {smpl for smpl in samples | |
if not smpl.startswith('BLANK')} |