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Clinical-Genomics / cg_lims

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EPP: prepare_new_samples.py #87

Closed barrystokman closed 2 years ago

barrystokman commented 3 years ago

Lims Issue

Work Flow: tbd Protocol: tbd Step: tbd

Description: Implement EPP prepare_new_samples.py

barrystokman commented 3 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']
barrystokman commented 3 years ago

Set Missing Reads/Set date and missing reads

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
barrystokman commented 2 years ago

Done: https://github.com/Clinical-Genomics/cg_lims/pull/90