Update tutorials to 0.9.x #16
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The tutorials on the documentation are out of date and do not run anymore. Following on the work from Workshop1 and Workshop 2, it's time to update these tutorials.
This work also stems and will fix #14.
They now include sample data (including a reference file) for the alignment workflow, and building Samtools flagstat uses the data that you get from tutorial 1 (so there's some continuity).
There is still work to be done which is documented in #6.