New version of Development WF

[mayabrandi]

Workflow Name: CG001 Development Projects

• [x] Add Quantit step to protocols CG002 Library validation QC (Dev) and to CG002 Initial QC (Dev). Can look like this: WF: WGS PCR free v4, protocol: Initial QC wgs v4 step: Quantit QC (DNA) WGS v1, but add button to calculate amount, remove button to set QC.
• [x] in Qubit step protocol Initial QC (Dev) v3

  add volume add buttoin to calculate amount show subbmitted sample lims id

• [x] in Tapestation step

  show lims id add button get size from file. (now it is on udf Average size (bp). but should be on Size (bp)) In both protocols CG002 Library validation QC (Dev) and to CG002 Initial QC (Dev)

• [x] check that aggregate step is fine
• [x] cg002 Libary Prep

  show submitted sample lims id

• [ ] default sequencing should be nova seq

  make sure the correct number are being fetched to the define step

[cesve]

@Mropat kan vi titta på Tapestation steget? Jag skulle vilja ha en "sample placement" i steget.

Scriptet "Get size (bp) funkar inte nu men jag tror det är för att proverna inte har placerats i en platta.

[cesve]

@Mropat vi behöver också "Sample placement" i Quantit. Det gör att script "Get concentration from result file" inte funkar.

Script "Calculate Amounts" sätter även QC, det vill vi inte. Den ska bara calculate amount.

[cesve]

@Mropat placement map-scriptet körs men filen sparas inte i steget: https://clinical-lims-stage.scilifelab.se/clarity/work-details/173002

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Initial QC (Dev) v3 Step: Tapestation Reception Control v3

• [x] Shows lims id in Sample Details.
• [x] Added script to get Size (bp) from csv-file.
• [x] Added UDF "Size (bp) in Sample Details.

Everything work as expected. Samples get their sizes, see picture. The csv-file is found in this: step

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Initial QC (Dev) v3 Step: Quantit QC (DNA) v1

• [x] Get concentration from file.
• [x] Placement map with original well and original container

Everything work as expected. Samples get their concentrations and Placement map is generated correctly, see pictures. The csv-file is found in this step

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Initial QC (Dev) v3 Step: Qubit QC (DNA) v3

• [x] UDF volume added in Sample Details.
• [x] Shows lims id in Sample Details.

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Initial QC (Dev) v3 Step: Aggregate QC (DNA) v3

Samples run in step Qubit QC (DNA) v3. Aggregation worked good.

Samples run in step Quantit QC (DNA) v1. Aggregation worked good.

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Library validation QC (Dev) v3 Step: Quantit QC (DNA) v1

• [x] Get concentration from file.
• [x] Placement map with source well and source container

Everything work as expected. Samples get their concentrations and Placement map is generated correctly, see pictures. The csv-file is found in this step

The "Calculate amount" script is verified here cg_lims #25

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Library validation QC (Dev) v3 Step: Tapestation QC v3

• [x] Shows lims id in Sample Details.
• [x] Added script to get Size (bp) from csv-file.
• [x] Added UDF "Size (bp) in Sample Details.

Everything work as expected. Samples get their sizes, see picture. The csv-file is found in this: step

[cesve]

Test 210129. Steps where changes have been made are shown below:

Protocol: Initial QC (Dev) v3 Step: Aggregate QC (DNA) v3

Samples run in step Qubit QC (Library Validation) v3. Aggregation worked good.

Samples run in step Quantit QC (DNA) v1. Aggregation worked good.

[Mropat]

Concentration copied successfully into files!