Added --save_intermediates #1322

Job	Run time
Choose nextflow versions to test against depending on target branch	1s
nf-test (latest-everything, test, docker)	32s
nf-test (latest-everything, test_single, docker)	25s
nf-test (latest-everything, test_fasta, docker)	32s
nf-test (latest-everything, test_failed, docker)	25s
nf-test (latest-everything, test_multi, docker)	22s
nf-test (latest-everything, test_reftaxcustom, docker)	46s
nf-test (latest-everything, test_qiimecustom, docker)	44s
nf-test (latest-everything, test_doubleprimers, docker)	27s
nf-test (latest-everything, test_iontorrent, docker)	25s
nf-test (latest-everything, test_novaseq, docker)	29s
nf-test (latest-everything, test_pacbio_its, docker)	24s
nf-test (latest-everything, test_sintax, docker)	25s
nf-test (latest-everything, test_pplace, docker)	25s
	6m 22s

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