Switching to rlog for deseq2 vs method truncates pipeline output about differentialabundance HOT 4 CLOSED

Hey @tfalkarkea, I just tried to reproduce that error with my local installation of diffab and did not manage to; all modules run for me. Unfortunately, your exact command does not work for me because of some stupid docker error, but I'm right now seeing if I can reproduce the error with singularity.
My nextflow version is newer than yours, however, so possibly that is what fixes this issue? Could you try updating to nextflow=23.10.0 and rerunning?

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Alright, with singularity the online pipeline version worked, but indeed it skipped some modules. Will see if I can figure out the reason

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Okay, so for some reason, the first time I used the command, nextflow pulled an old version, just as it did for @tfalkarkea (nf-core/differentialabundance v1.2.0-g3a849f0; I think for me it was version 1.2.1). I'm not sure why this happens as it should actually default to the newest version, which is 1.3.1. You can ensure that that version is run by adding -r 1.3.1 to your execution command, then everything should run fine :) I will close this for now, please do re-open if it does not work for you!

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Thanks for taking a look! Glad it could be fixed.

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