Open EmiliaRegazzoni opened 2 years ago
idalindegaard
commented
1 year ago Very good idea. The script that gets the values from the CSV files is hardcoded i.e., need the exact name of the placeholder. Therefore I need to check this before just changing the name so no problems will arise
idalindegaard
commented
1 year ago @EmiliaRegazzoni I've checked each step and tried running the scripts with new placeholder names, but it seems that all the scripts need the placeholders to have the specific names that we have currently. When I've learned how to change in scripts I can correct this and update in LIMS
KSV is updating the qPCR Result file script and will remove the hardcoding of the placeholder name
Lims Issue
For definitions of headings below see Basic Concepts.
Work Flow: WGS PCR free v5 Protocol: Library validation QC wgs v3 Step: CG002 - qPCR QC (Library Validation) CURRENT FILE NAME: qPCR Result File SUGGESTED FILE NAME: Quantification Summary
Work Flow: RNA v3 Protocol: Library Validation QC RNA (post norm) Step: Tapestation QC (RNA) CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Work Flow: RNA v3 Protocol: Library Validation QC (RNA) Step: Tapestation QC (RNA) CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Work Flow: RNA v3 Protocol: Initial QC (RNA) v2 Step: Tapestation Reception Control (RNA) CURRENT FILE NAME: Tapestation RIN CSV SUGGESTED FILE NAME: Sample Table CSV (RIN)
Work Flow: TWIST v7 Protocol: Initial QC TWIST v3 Step: Tapestation Reception Control TWIST CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table CURRENT FILE NAME: Tapestation DIN CSV SUGGESTED FILE NAME: Sample Table CSV (DIN)
Work Flow: TWIST v7 Protocol: Library Validation QC TWIST v2 Step: Tapestation QC TWIST CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Work Flow: TWIST v7 Protocol: Library Validation QC TWIST (post hyb) Step: Tapestation QC TWIST CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Work Flow: TWIST v7 Protocol: Library Validation QC TWIST (post norm) Step: Tapestation QC TWIST CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Work Flow: Microbial WGS v6 Protocol: Microbial Library Validation QC v3 Step: CG002 - Tapestation Microbial QC CURRENT FILE NAME: Tapestation CSV SUGGESTED FILE NAME: Compact Region Table
Description: For several steps in lims (in multiple work flows) the file names in lims do not correspond to the actual names for the files produced by the instruments. It would be easier for people working in production if they were identical, limiting the confusion about which file is which. I have tried to identify the steps in which this is the case above. This issue relates to deviation "Wrong final concentration applied to wgs libraries" #309: https://github.com/Clinical-Genomics/Deviations/issues/309.