Move process config into pipeline code #1913

Job	Run time
Run pipeline with test data (22.10.1)	44s
Run pipeline with test data (latest-everything)	39s
Test STAR RSEM with workflow parameters (--skip_qc)	41s
Test STAR RSEM with workflow parameters (--rsem_index false)	48s
Test STAR Salmon with workflow parameters (--skip_qc)	43s
Test STAR Salmon with workflow parameters (--skip_trimming)	38s
Test HISAT2 with workflow parameters (--skip_qc)	37s
Test STAR Salmon with workflow parameters (--gtf false)	45s
Test HISAT2 with workflow parameters (--hisat2_index false)	48s
Test STAR Salmon with workflow parameters (--star_index false)	40s
Test Salmon with workflow parameters (--skip_qc)	45s
Test STAR Salmon with workflow parameters (--transcript_fasta false)	40s
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)	49s
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)	34s
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)	53s
Test STAR Salmon with workflow parameters (--with_umi)	47s
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)	44s
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)	35s
Test STAR Salmon with workflow parameters (--bam_csi_index)	36s
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)	48s
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)	43s
Test STAR Salmon with workflow parameters (--trimmer fastp)	47s
	15m 44s

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