Not looking to start a debate on #nextflow vs. #snakemake, but curious about their ease of adoption in a typical lab setting with ~4-year PhD/postdoc turnover. How do you feel newcomers adapt to each? Would you recommend one for easier onboarding? Feedback appreciated! #genomics #bioinformatics - ThreadSky

manolis-maragkakis.bsky.social • 77 days ago

Not looking to start a debate on #nextflow vs. #snakemake, but curious about their ease of adoption in a typical lab setting with ~4-year PhD/postdoc turnover. How do you feel newcomers adapt to each? Would you recommend one for easier onboarding? Feedback appreciated!
#genomics #bioinformatics

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joepdel.bsky.social•77 days ago

For me both fall in the 'easy to learn, hard to master' grouping for early career researchers. And recommend having at least 1 more permanent staff to support this. @nextflow.io has the biggest community/more resources to grab a pre existing pipeline.

manolis-maragkakis.bsky.social•76 days ago

Thanks. 👀 seems I'm the most permanent staff. Coming from snakemake, maybe time to dive into nextflow as well 😅

arcane-mahesh.bsky.social•77 days ago

Usually people are really interested in learning something new, especially if someone experienced can show how these tools make their life easier. Have regular meetings/training so people talk to each other and don't try and do things in isolation. For #Nextflow, join the communities too.

arcane-mahesh.bsky.social•77 days ago

My point is it's the learning environment rather than the tools in my opinion. Since we all suffer from imposter syndrome to some degree, the ease with which we can ask questions and get positive responses regardless of skill level is what makes adoption easier.

evilution.bsky.social•76 days ago

Do you already have knowledge in one? My opinion is a PI should have working knowledge in the DSL as PI will be the constant.

There isn’t a “bad” choice in either of these.

What are your compute resources? HPC? Cloud? Neither? I’d also see which ones supports your comp env requirements.

manolis-maragkakis.bsky.social•76 days ago

Yes I do use snakemake regularly but that's only because I found it a bit easier for my workflow several years back. Mostly HPC.

bradbowles.bsky.social•76 days ago

As Nextflow newcomer, I think Nextflow is well documented and I’ve found it easier to learn than Snakemake as a result. The NF-core repo has also provided a large number centralized, curated examples for me as a learner. Can’t say which is better, but NF has been beginner-friendly in my experience.

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