Added --save_intermediates #1319

Job	Run time
Choose nextflow versions to test against depending on target branch	1s
nf-test (latest-everything, test, docker)	19m 53s
nf-test (latest-everything, test_single, docker)	5m 44s
nf-test (latest-everything, test_fasta, docker)	2m 50s
nf-test (latest-everything, test_failed, docker)	14m 56s
nf-test (latest-everything, test_multi, docker)	8m 57s
nf-test (latest-everything, test_reftaxcustom, docker)	7m 0s
nf-test (latest-everything, test_qiimecustom, docker)	6m 55s
nf-test (latest-everything, test_doubleprimers, docker)	9m 23s
nf-test (latest-everything, test_iontorrent, docker)	5m 23s
nf-test (latest-everything, test_novaseq, docker)	3m 37s
nf-test (latest-everything, test_pacbio_its, docker)	8m 28s
nf-test (latest-everything, test_sintax, docker)	16m 22s
nf-test (latest-everything, test_pplace, docker)	11m 34s
	2h 1m 3s

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