At first glance at the nf-core (NextFlow) pipeline seqinspector, it seemed obvious that it needed to include FastQ-Screen.
However, the dev branch actually does include it. So the next question was, how do you run nf-core workflows on specific branches?
Previous-efforts-write-up:
For the query "how do I specify an nf-core workflow branch?", Google AI suggested the realistic looking but false --branch dev, which was suspicious because NextFlow-specific options typically have two dashes.
But even the slightly modified -branch dev did not work either.
The AI suggested sources weren't helpful either and neither were the various search hits I tried.
Answer
The option* you want to use: -r dev
Note that this is a standard NextFlow feature, not something specific to nf-core:
Any Git branch, tag, or commit of a project repository can be used when launching a pipeline by specifying the
-roption:
nextflow run nextflow-io/hello -r mybranch
*Thanks to an individual from the #seqinspector channel of the nf-core Slack workspace. Your explanation was the first hit to my in-Slack query in:#seqinspector run dev . It sure is nice to see real humans still asking and answering questions.
By the way, after finding the right answer from a human-based source, I found out that if I added "Assume that I need this by tomorrow" or "Assume that you are an experienced bioinformatician" to my original query that it worked.
On the otherhand, "Assume that you are very experienced using nf-core" still gave me the spurious --branch answer.