The tests are too slow

[marcelm]

During development, I regularly run all tests to see whether my changes did not introduce any regressions. This is at the moment very slow (a couple of minutes), making development also slow.

The tests in test_cli.py should be changed to not run the full pipeline.

[marcelm]

pytest --durations 0 outputs:

========= slowest test durations 
28.15s call     tests/test_cli.py::test_call_variants[gatk]
25.20s call     tests/test_cli.py::test_BQSR
23.14s call     tests/test_cli.py::test_plot_figures
21.89s call     tests/test_cli.py::test_call_variants[bcftools]
21.35s call     tests/test_cli.py::test_haplotag[whatshap]
21.34s call     tests/test_cli.py::test_haplotag[blr]
18.67s call     tests/test_cli.py::test_call_variants[freebayes]
15.99s call     tests/test_cli.py::test_final_compressed_reads_exist
9.45s call     tests/test_cli.py::test_mappers[bowtie2]
6.53s call     tests/test_cli.py::test_mappers[ema]
5.96s call     tests/test_cli.py::test_mappers[bwa]
5.67s call     tests/test_cli.py::test_mappers[minimap2]
3.62s call     tests/test_cli.py::test_trim_blr
2.28s call     tests/test_cli.py::test_trim_stlfr
1.01s call     tests/test_cli.py::test_trim_tenx
...
======== 18 passed in 210.93s (0:03:30)