Integrate subworkflows into pipeline #1292

Job	Run time
24.04.2 \| test \| docker	10m 30s
24.04.2 \| nogtf \| docker	8m 2s
24.04.2 \| affy \| docker	9m 18s
24.04.2 \| maxquant \| docker	7m 36s
24.04.2 \| soft \| docker	7m 14s
24.04.2 \| rnaseq_limma \| docker	7m 12s
latest-stable \| test \| docker	9m 49s
latest-stable \| nogtf \| docker	7m 29s
latest-stable \| affy \| docker	9m 10s
latest-stable \| maxquant \| docker	6m 54s
latest-stable \| soft \| docker	5m 59s
latest-stable \| rnaseq_limma \| docker	7m 14s
	1h 36m 27s

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