Occasionally our negative control sample won't make it all the way through our artic pipeline. This seems to usually happen because all reads are filtered out during the dehosting/adapterfiltering/readtrimming stages, so no reads remain to produce an alignment.
When that happens, we get an entry in our config.yaml file like:
negative_control_samples: [""]
...and the pipeline fails.
If no negative control sample is found, omit the negative_control_samples line from the config.yaml
Occasionally our negative control sample won't make it all the way through our artic pipeline. This seems to usually happen because all reads are filtered out during the dehosting/adapterfiltering/readtrimming stages, so no reads remain to produce an alignment.
When that happens, we get an entry in our
config.yamlfile like:...and the pipeline fails.
If no negative control sample is found, omit the
negative_control_samplesline from theconfig.yaml