Fixes MISO scratch/launch directory and gffread issue #226

Job	Run time
Run full pipeline with test data (23.04.0)	42m 34s
Run full pipeline with test data (latest-everything)	35m 54s
Run DEXSeq pipeline with test data (23.04.0)	28m 37s
Run DEXSeq pipeline with test data (latest-everything)	31m 36s
Run edgeR pipeline with test data (23.04.0)	19m 45s
Run edgeR pipeline with test data (latest-everything)	19m 12s
Run full pipeline with FASTQ data (23.04.0)	39m 15s
Run full pipeline with FASTQ data (latest-everything)	33m 50s
Run full pipeline with genome BAM data (23.04.0)	22m 9s
Run full pipeline with genome BAM data (latest-everything)	19m 10s
Run rMATS pipeline with test data (23.04.0)	20m 16s
Run rMATS pipeline with test data (latest-everything)	24m 30s
Run full pipeline with Salmon results data (23.04.0)	4m 52s
Run full pipeline with Salmon results data (latest-everything)	5m 48s
Run SUPPA pipeline with test data (23.04.0)	21m 0s
Run SUPPA pipeline with test data (latest-everything)	25m 54s
Run full pipeline with transcriptome BAM data (23.04.0)	6m 0s
Run full pipeline with transcriptome BAM data (latest-everything)	6m 34s
	6h 46m 56s

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