Checkqc

This release adds two major features. The first is a new way of running CheckQC - now it is possible to run it as a webservice as well as a normal command line application.

To run CheckQC as a webservice, use the following command:


checkqc-ws <path to directory with runfolders>


The second feature is a json-mode for the cli. Adding `--json` when running CheckQC will print the output of the program as json to stdout. This is e.g. useful if you want to pass the CheckQC output to other programs to futher parse the data.

In addition to these feature the following minor features are also part of this relase.
- Validation of handler config
- CheckQC will now raise an error if there is no error rate present in a run (e.g. because no PhiX was added to the lane). This behaviour can be overridden by setting `allow_missing_error_rate: True` in the `ErrorRateHandler` part of the config.
- Added commandline option to print the program version

Enjoy!

This is the `1.0.0` release of CheckQC. :fireworks:

Running CheckQC is as easy as:


checkqc <path to your runfolder>


In this version CheckQC supports the following Illumina instruments:

- HiSeqX
- HiSeq2500
- MiSeq
- NovaSeq

It has five handlers which allows examining the following QC metrics:
- `UndeterminedPercentageHandler`, checks the amount of reads which could not be assigned to a specific sample.
- `ClusterPFHandler`, checks the amount of clusters (reads) which have passed Illuminas filters.
- `Q30Handler`, checks the percentage of data which is above Q30.
- `ErrorRateHandler`, checks that the error rate is below a set value
- `ReadsPerSampleHandler`, checks that the number of reads assigned to a sample is not below what one would expect given the number of samples on that lane (assuming that all samples pooled together should have the same amount of data)

Enjoy!