i'm baffled new pipelines are still being built......
# riboseq_devi
Ira Iosub
10/18/2026, 2:44 PMi'm baffled new pipelines are still being built.... even now w nf-core/riboseq already at 2nd major release. i am also not sure the configurability of the pipeline is accurately represented here biorxiv.org/content/10.64898/…
😲 1
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Jack Tierney
11/06/2026, 9:28 AMCan Cenik was actually involved in the initial proposal for the creation of nf-core/riboseq along with Ed Wallace
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Ira Iosub
11/06/2026, 2:22 PMyes, this is why I find this even more surprising. Do you think it’s worthwhile to maybe contact him and kindly ask to correct/adjust some of the statements re configuration of mapping? I feel for both nf-core/riboseq and riboseq-flow the way these are described does not reflect the capabilities of the pipelines
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Jack Tierney
11/06/2026, 2:23 PMI need to look into what you mean by that but I am sure he would be receptive.
Jack Tierney
11/06/2026, 2:23 PMHe reviewed Riboseq-flow too right?
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Ira Iosub
11/06/2026, 2:24 PMyes, he did also
Ira Iosub
11/06/2026, 2:26 PMmy impression was the text was suggesting previous pipelines aren’t flexible regarding multimapper settings/handling - i’ll have a look again to make sure; similarly there was some criticism raised re P-site identification, but my impression is the new pipeline doesn’t solve that aspect either.
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Jack Tierney
11/06/2026, 2:41 PMJust had a quick skim of it and I agree with you on both points. The alignment parameters especially needs to be corrected