Test runner: caching, parallelization, test selection

[dennishendriksen]

$ bash test.sh --test cram/single,cram/trio,cram/multi* --clean
running tests ...
cram/multiproject                        | PASSED | 141853=completed output/cram/multiproject/.nxf.log
cram/single                              | PASSED | 141854=completed output/cram/single/.nxf.log
cram/trio                                | PASSED | 141855=completed output/cram/trio/.nxf.log
done

$ bash test.sh --test vcf --clean
running tests ...
vcf/corner_cases                         | PASSED | 141944=completed output/vcf/corner_cases/.nxf.log
vcf/empty_input                          | PASSED | 141945=completed output/vcf/empty_input/.nxf.log
vcf/empty_output_filter_samples          | PASSED | 141946=completed output/vcf/empty_output_filter_samples/.nxf.log
vcf/empty_output_filter                  | PASSED | 141947=completed output/vcf/empty_output_filter/.nxf.log
vcf/lb_b38                               | PASSED | 141948=completed output/vcf/lb_b38/.nxf.log
vcf/lb                                   | PASSED | 141949=completed output/vcf/lb/.nxf.log
vcf/lp_b38                               | PASSED | 141950=completed output/vcf/lp_b38/.nxf.log
vcf/lp                                   | PASSED | 141951=completed output/vcf/lp/.nxf.log
vcf/multiproject_classify                | PASSED | 141952=completed output/vcf/multiproject_classify/.nxf.log
vcf/snv_proband                          | PASSED | 141953=completed output/vcf/snv_proband/.nxf.log
vcf/snv_proband_trio_b38                 | PASSED | 141954=completed output/vcf/snv_proband_trio_b38/.nxf.log
vcf/snv_proband_trio_sample_filtering    | PASSED | 141955=completed output/vcf/snv_proband_trio_sample_filtering/.nxf.log
vcf/snv_proband_trio                     | PASSED | 141956=completed output/vcf/snv_proband_trio/.nxf.log
done

[umcg-dhendriksen@betabarrel test]$ bash test.sh --test fastq --clean
running tests ...
fastq/nanopore                           | PASSED | 142143=completed output/fastq/nanopore/.nxf.log
fastq/pacbio_hifi                        | PASSED | 142144=completed output/fastq/pacbio_hifi/.nxf.log
done