Major release with the following updates included
0.19.* UPDATES
27: Bugfix, minimap uses now different tmp suffixes for different jobs
26: Script getFastaFromVCF could create negative coordinatethat leaad to an error, fixed.
25: transanno added to minimap2 docker image and updated to version 2.26
24: Improvement for Bugfix 0.19.18, there was a copy+paste error that prevented the bugfix to work properly
23: CRITICAL Bugfix: There was a bug in the in-silico size-selection script, leading to a wrong in-silico reference genome
22: The overhang of the restriction enzymes can now be provided
21: Updated the in-silico digestion script, as it contained apparently a little bug in the SimRAD package
20: Added a heatmap function to summarize the quantification locations on the reference genome.
19: Reintroduced the image visualisation of te VCF image
18: Bugfix, the pipeline crashed when no sampleinfo.tsv file was given
17: Bugfix, sampleinfo colnames caused an error in the casecontrol part, that is fixed now.
16: Dependency adjusted for mock alignment against reference genome in finalReport
15: Bugfix, when only one group information was provided in samplinfo.tsv the finalReport crashed
14: Added the liftOver rules to liftover the finalMock based VCF to an existing reference genome
13: The mock references are now also fa-indexed
12: Added --eqx option to minimap steps, as the "assert(has_cigar + no_cigar == 1);" test failed sometimes
11: Now I write down the mock to insilico mapping rates
10: Changed the index for Mock vs insilico to bai from csi, as csi threw an error for the mock reference
9: Adjusted the file paths to the log file
8: Mock reference is now also aligned against the different in-silico predictions
7: Removed the previous additions and started an own similarity metric script instead.
6: Added the mock to reference similarity step, using MUMmer
5: Enabled the SE option, so the pipeline should now be ready to handle also single-end input (not in the reports, yet)
4: Handled the case that no reads were disgarded from the mock reference building step
3: Removed minimum lengths criteris in pear command
2: Use N for stitching instead of T
1: New dev branch