@Mark Pampuch I’ve used most of my free time this week to fix the issues I could spot and I’ve merged a PR to dev to: • make sure it runs on seqera platform (the issue was a silly missing space / newline between code and comment which doesn’t trigger an error in Nextflow but apparently does when Seqera platform parses the config) • a much more important fix to a Java NPE error, which only happens with versions 25.x of Nextflow (can’t figure out the reason, but it’s fixed) • full test run (I’ve tested on Seqera platform using our GCP environment, as well as local HPC): please notice here the R report has failed due to wall-time and I purposedly set the error strategy to

ignore

instead of

retry

. the report on the pipeline has always been intended to be more a parsing of the outputs rather than a proper analysis, due to the difficulty in generalising how people use the data • template has been updated to nf-core version 3.3.2 (which is not the latest one): there is still an impossible for me to understand linting error, which is only thrown in the PR github action and not in the

nf-core pipelines lint

run on the devcontainer, flagging a difference in the PR template file: this is irrelevant to pipeline functionality all of this is in dev, so if you wish to run from Seqera please make sure you select the

dev

branch or run Nextflow with

-r dev

besides all this maintenance stuff, we’re of course available to discuss any science-based collaboration of course.