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| elif len(species) < 1: | ||
| run_type = "" | ||
| else: | ||
| elif i.split("-")[1].startswith("SH"): |
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Will this mess things up if we run other organisms on the i100s?
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Good catch I could update this to include & len(species) < 1. This way if there is not information in Clarity it won't call 'Granduer' and run the analysis on sample that don't need it. The only downside is the automation would not work if not tracked in Clarity or if for some reason the "Run_names" differs from whats in Clarity. Status quo would catch more false positives while the proposed alternative would have more false negatives. I think either works.
erinyoung
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erinyoung
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This seems to be running fine, so I approve this PR.
From what I gather, grandeur is set up to run on all the miseq i100 runs. Right now I don't think that's a problem.
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This pull request updates analysis_for_run.py and screen_run.py to run a new script grandeur_aws_automation.py. Currently the three scripts try to accomplish what is outlined below.
analysis_for_run.py - identifies new runs using the BS CLI tool. It looks for 'Species' information about the run on Clarity. It sends a message to Slack about the new run and what samples are in it if found. It then starts another screen to run screen_run.py and passes a run type argument, mycosnp if the run has 'Candida' samples found on Clarity and grandeur if the run is on Miseqi100.
screen_run.py uses the BS CLI tool to monitor the run and send a Slack Message when the run is completed then kick off any automation that exists (Currently only granduer) to run on the same screen as screen_run.py is ran on.
grandeur_aws_automation.py- moves fastq files and Samplesheet from sequencer output folder in NGS to the analysis folder in NGS_2/pulsenet_and_arln/. Creates samplesheet for Grandeur. Uploads reads and granduer samplesheet to AWS Prod account. Creates json file that AWS uses to initialize run and uploads it to AWS. Monitors the run on AWS till it finishes where it then downloads the analysis output and logs. It updates the Slack channel when AWS analysis begins and when it ends and download begins.