Added separate param for setting qval threshold for pathway analysis #1128

Job	Run time
Run pipeline with test data (23.04.0)	3m 32s
Test workflow parameters (test)	6m 0s
Run pipeline with test data (latest-everything)	3m 6s
Test workflow parameters (test_full)	4m 46s
Test workflow parameters (test_contrast_matrix)	2m 38s
Test workflow parameters (test_contrast_list)	3m 43s
Test workflow parameters (test_no_multiqc)	2m 46s
Test workflow parameters (test_relevel)	2m 53s
Test workflow parameters (test_smrnaseq)	2m 47s
Test workflow parameters (test_star_rsem)	6m 0s
Test workflow parameters (test_star_salmon)	4m 47s
Test workflow parameters (test_use_vst)	2m 32s
Test workflow parameters (test_batcheffect)	2m 54s
Test workflow parameters (test_custom_gmt)	3m 28s
	51m 52s

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