Move process config into pipeline code #1889

Job	Run time
Run pipeline with test data (22.10.1)	42s
Run pipeline with test data (latest-everything)	53s
Test STAR RSEM with workflow parameters (--skip_qc)	38s
Test STAR Salmon with workflow parameters (--skip_qc)	35s
Test STAR RSEM with workflow parameters (--rsem_index false)	41s
Test STAR Salmon with workflow parameters (--skip_trimming)	42s
Test STAR Salmon with workflow parameters (--gtf false)	47s
Test STAR Salmon with workflow parameters (--star_index false)	39s
Test STAR Salmon with workflow parameters (--transcript_fasta false)	50s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)	35s
Test STAR Salmon with workflow parameters (--with_umi)	41s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)	46s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)	34s
Test STAR Salmon with workflow parameters (--bam_csi_index)	39s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)	36s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)	34s
Test STAR Salmon with workflow parameters (--trimmer fastp)	33s
Test HISAT2 with workflow parameters (--skip_qc)	35s
Test Salmon with workflow parameters (--skip_qc)	56s
Test HISAT2 with workflow parameters (--hisat2_index false)	38s
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)	40s
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)	49s
	15m 3s

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