Final step of my pipeline halts succesfully after 1 sample

[Malarkey73 (Stephen Henderson)]

Sorry I think I’ve found the answer earlier on this forum to the same question:

Pipeline only processes first element of channel

Whenever you have a process with two or more input channels and this process is not running for all elements of one of the channels, the first thing that must come to mind are the concepts of queue and value channels. Queue channel elements are consumed only once, while the value channel element can be consumed numerous times. Let’s think of two queue channels with the following elements: FirstChannel has A, B and C as elements SecondChannel has D and E. If we provide these two channels as in…

Groovy doesn’t recycle. My input should be:

ichorcna(readcounter.out.wig, centromere_ch.first(), gcwig_ch.first(), mapwig_ch.first(), normpanel_ch.first())

Apologies for not spotting the earlier answer.

S