Expansion of LIMS issue - Simplify moving between steps in lims

[AbiDalby]

Lims Issue

For definitions of headings below see Basic Concepts.

Work Flow: All workflows
Protocol: All protocols (excluding QC steps, or skip steps)
Step: All steps (excluding QC steps, or skip steps)

Description: Discussions while working on the LIMS issue here lifted the possibility of easing moving between steps in all lims workflows and protocols where all samples proceed to the next step or protocol.

This excludes all QC protocols as samples can fail QC and these samples should be handled manually without the risk of them moving to the next step/protocol in the workflow.

Steps that have an automation for skipping over steps or to the next protocol (e.g. skip buffer exchange) are also excluded as the lab person needs to double-check that the correct samples are assigned to skip, while the other samples aren't.

Firstly, we are looking into the final step of all non-QC protocols to have an EPP that runs automatically when moving from "Record Details" to "Next Steps" which automatically assigns "Mark protocol as complete" into the "Next Step" field.

• New EPPs (Set Next Steps X) generated to account for the differing number of Step File Placeholders in each step
• Combined EPPs Atlas Method Document and Set Next Steps to allow for the EPP to run automatically upon exiting "Record Details" when there are several other EPPs in the step.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid3} && conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set method-document -pru 'Library Preparation Method' -pru 'Library Preparation Method 1' -pru 'Library Preparation Method 2' -pru 'Supporting Procedure Document' -pru 'Supporting Procedure Document 1' -pru 'Supporting Procedure Document 2' -pru 'Equipment Document' -pru 'Equipment Document 1' -pru 'Equipment Document 2' -pru 'Sequencing Method' -pru 'Library preparation method'"

• Combine EPPs "Set Library Preped Date" and "Set Next Steps 0" to make a new EPP.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid0} && conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf set set-sample-date --sample-udf 'Library Prep Finished'"

• Combine EPPs "Calculate Missing Reads For Pools" and "Set Next Steps" to make a new EPP.

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -exp 'nextStep = ::ADVANCE::' -log {compoundOutputFileLuid4} && conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid4} -p {processLuid} udf calculate missing-reads-in-pool"

• Test each step after making changes and document these by taking a screenshot.

Results:

1. New working EPP "Atlas Method Document and Set Next Steps" used in Step "CG002 - Normalization of microbial samples for sequencing"

2. New working EPP "Set Library Prepped Date and Set Next Steps" used in Step "Pool samples NIPT v2"

3. New working EPP "Calculate Missing Reads For Pools and Set Next Steps" used in step "Pooling and Clean-up (Cov) v1"