idalindegaard
commented
6 months ago I created a new EPP called Copy Concentration (nM) for Sequencing
bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy artifact-to-artifact -n 'Library Prep (Dev) v3' -n 'CG002 - RML Library Pooling' -n 'Normalization of RNA samples for sequencing v1' -n 'Pooling and Clean-up (Cov) v1' -n 'Normalization of pool for sequencing (Cov) v1' -n 'Bead Purification TWIST v2' -n 'Normalization of samples for sequencing (TWIST) v1' -n 'Normalization of samples for sequencing (TWIST) v2' -n 'End repair Size selection A-tailing and Adapter ligation (TruSeq PCR-free DNA)' -n --sample-artifact -au 'Concentration (nM)'; conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy process-to-artifact -audf 'Concentration (nM)' -pudf 'Final Concentration (nM)' -n 'CG002 - Normalization of microbial samples for sequencing'"
And tested it in step Define Run Format and Calculate Volumes (NovaSeq X)
The new EPP can fetch all concentrations now in one click but an error message is generated since the two scripts that have been merged in one EPP will "complain" about the samples that they are not accounting for.
This would need to be fixed
Lims Issue
For definitions of headings below see Basic Concepts.
Work Flow: NovaSeq X v1 Protocol: NovaSeq X v1 Step: Define Run Format and Calculate Volumes (NovaSeq X)
Description:
There are two EPPs for retrieving library concentrations (nM) in step Define Run Format and Calculate Volumes (NovaSeq X), where the one fetching microbial concentrations is separated from the rest. It would be convenient to merge this into one.
Suggestion: Merge Copy Concentration (nM) from Library Preparation or Sample-Artifact and Copy Concentration (nM) (Microbial) into Copy Concentration (nM) for Sequencing