Closed barrystokman closed 2 years ago
(cg_lims) bash-4.2$ python opt/clinical_EPPs/clinical_EPPs/check_configuration.py -s prepare_new_samples.py
INFO:AUTOMATION: Searching for 'prepare_new_samples.py'.
INFO:Button: Set Missing Reads
INFO:Bash string: bash -c "/home/glsai/miniconda3/envs/epp_master/bin/prepare_new_samples.py -p {processLuid}"
INFO:Processes: ['679', '912', '1070', '1154', '1204', '1213', '1370', '1413', '1424']
INFO:AUTOMATION: Searching for 'prepare_new_samples.py'.
INFO:Button: Set date and missing reads
INFO:Bash string: bash -c -l "conda activate cg_lims && lims -c /home/glsai/.genologics.yaml epps -l {compoundOutputFileLuid0} -p {processLuid} udf copy process-to-sample -sudf 'Received at' -pudf 'date arrived at clinical genomics' && /home/glsai/miniconda3/envs/epp_master/bin/prepare_new_samples.py -p {processLuid}"
INFO:Processes: ['679', '912', '1070', '1154', '1204', '1213', '1370', '1413', '1424']
Automation use enabled here: Master Steps -> Steps -> Protocols -> Workflows (active only):
# | Master Step | Step | Protocol | Workflow | Set Missing Reads | Set date and missing reads |
---|---|---|---|---|---|---|
1. | CG002 - Reception Control | CG002 - Reception Control | CG002 - Reception Control | RML v6 | N | Y |
2. | CG002 - Reception Control | Reception Control NIPT | Reception Control NIPT v1 | NIPT v1 | N | Y |
3. | CG002 - Reception Control | Reception Control v3 | Initial QC wgs v4 | WGS PCR free v5 | N | Y |
4. | Reception Control v2 | |||||
5. | Reception Control (RNA) v1 | Reception Control (RNA) | Initial QC (RNA) | RNA v2 | N | Y |
6. | Reception Control no placement v2 | Reception Control TWIST | Pre Processing TWIST v2 | TWIST v4 | N | Y |
7. | Reception Control (Dev) v3 | Reception Control (Dev) | Initial QC (Dev) v3 | Development Projects v3 | N | Y |
8. | Reception Control (Cov) v1 | Reception Control (Cov) | Initial QC (Cov) v1 | SARS-CoV-2 v3 | N | Y |
9. | Reception Control TWIST v1 | |||||
10. | CG002 - Reception Control (Dev) | |||||
11. | Reception Control no placement v1 | Reception Control | Pre Processing Microbial v1 | Microbial WGS v6 | N | Y |
Lims Issue
Work Flow: tbd Protocol: tbd Step: tbd
Description: Implement EPP
prepare_new_samples.py