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cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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Add `HIV-AD` project definition #1191

Open Donaim opened 3 weeks ago

Donaim commented 3 weeks ago

In v7.17 we introduced HIV-AD project code.

But we haven't updated micall/projects.json file.

Because of this, updates to QAI fail with:

Failed to load project seeds for proj1 in date1.
Traceback (most recent call last):
  File "/usr/local/share/MiCall/micall/monitor/update_qai.py", line 115, in build_conseqs
    seeds |= projects.getProjectSeeds(target_project)
  File "/usr/local/share/MiCall/micall/core/project_config.py", line 136, in getProjectSeeds
    for region in self.config['projects'][project_name]['regions']:
KeyError: 'HIV-AD'

To solve this issue, we need to update the projects.json file.