add pipeline level tests #6257

Job	Run time
Check for changes (nf-test)	4s
Check for changes (pytest)	3s
pipeline_sarek test,docker NF	10m 14s
default docker NF 23.04.0	5m 56s
default docker NF latest-everything	6m 56s
tumor_normal_pair docker NF 23.04.0	5m 27s
tumor_normal_pair docker NF latest-everything	7m 17s
save_mapped_only docker NF 23.04.0	6m 29s
save_mapped_only docker NF latest-everything	5m 37s
save_output_as_bam_only docker NF 23.04.0	7m 19s
save_output_as_bam_only docker NF latest-everything	5m 39s
skip_all_qc docker NF 23.04.0	7m 53s
skip_all_qc docker NF latest-everything	5m 35s
skip_markduplicates docker NF 23.04.0	10m 46s
skip_markduplicates docker NF latest-everything	9m 36s
validation_checks docker NF 23.04.0	4m 47s
validation_checks docker NF latest-everything	2m 40s
alignment_from_everything docker NF 23.04.0	10m 21s
alignment_from_everything docker NF latest-everything	7m 54s
fastp docker NF 23.04.0	9m 42s
fastp docker NF latest-everything	6m 54s
cache docker NF 23.04.0	6m 27s
cache docker NF latest-everything	4m 56s
merge docker NF 23.04.0	6m 10s
merge docker NF latest-everything	9m 18s
snpeff docker NF 23.04.0	7m 38s
snpeff docker NF latest-everything	6m 59s
confirm-pass	1s
	2h 58m 38s

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