Final step of my pipeline halts succesfully after 1 sample

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1

Hello

I made pipeline that runs fastqc, hisat2 and a couple more steps successfully for a pair of test samples.

However the final step successfully runs for 1 sample and reports it has run [1/1 100%]. That output is correct. The prior step readcounter creates a wig file succesfully for both samples [2/2 100%].

So there is no error I see in the .nextflow.log. It just doesn’t start the 2nd job. Don’t know why.

my workflow input for the final step (in nextflow.config) is:

…

centromere_ch = Channel.fromPath(“assets/GRCh38.GCA_000001405.2_centromere_acen.txt”, checkIfExists: true)
gcwig_ch = Channel.fromPath(“assets/gc_hg38_1000kb.wig”)
mapwig_ch = Channel.fromPath(“assets/map_hg38_1000kb.wig”)
normpanel_ch = Channel.fromPath(“assets/HD_ULP_PoN_hg38_1Mb_median_normAutosome_median.rds”)
ichorcna(readcounter.out.wig, centromere_ch, gcwig_ch, mapwig_ch, normpanel_ch)

…

and my last step ichorcna module file input is

…

input:

path(wig)
path(centromere)
path(gcwig)
path(mapwig)
path(normalpanel)

…

Am I doing something wrong here?

2

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

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

3

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