Make it possible to skip MultiQC #140
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As seen in `workflows/demultiplex.nf`, when neither trimming nor fastq are skipped, md5 sums will only be generated for fastp files.
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maxulysse
reviewed
Aug 24, 2023
edmundmiller
approved these changes
Aug 24, 2023
workflows/demultiplex.nf
Outdated
| @@ -21,7 +21,7 @@ def checkPathParamList = [ | |||
| for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } | |||
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| // Check mandatory parameters | |||
| if (params.input) { ch_input = file(params.input) } else { Nextflow.error 'Input samplesheet not specified!' } | |||
| if (params.input) { ch_input = file(params.input) } else { error 'Input samplesheet not specified!' } | |||
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Interested why you removed the Nextflow.errors?
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Good question, when I run it (e.g. by removing a column in the input samplesheet), I get No such variable: Nextflow, when I remove Nextflow I get the correct error message. Maybe you could try it on your side to confirm this is not because of some glitch in my setup?
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What Nextflow version are you on? Here's the commit that changed it: d271419
@adamrtalbot Could you explain it?
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@adamrtalbot Could you explain it?
Honestly, no! If it doesn't import Nextflow and error works then go for it! Could be a good chance to add an explicit test for correctly raising an error.
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Other way around, @Aratz was finding Nextflow.error didn't work outside of a workflow context.
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That would make sense, we have to import the Nextflow class in the groovy files I think...
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I see the misunderstanding.
nextflow.Nextflow.error: Already imported into the namespace by Nextflownextflow.Nextflow: Not in namespace, but can be manually imported if you really want to (but really, don't).nextflow: Not in namespace, but can be manually imported if you really want to (but really, don't).
For those that would prefer examples:
This will not work
Here because Nextflow is not in the namespace:
def testError() {
Nextflow.error "Exiting due to an error"
}
workflow {
testError()
}The following will all work
Here we give the full namespace:
def testError() {
nextflow.Nextflow.error "Exiting due to an error"
}
workflow {
testError()
}Here because we import Nextflow into the namespace:
import nextflow.Nextflow
def testError() {
Nextflow.error "Exiting due to an error"
}
workflow {
testError()
}The two "working" examples are only provided for pedagogical purposes. They should always be abandoned in favour of the example below, where we rely on Nextflow importing nextflow.Nextflow.error into namespace for us:
and of course, the best and correct way:
def testError() {
error "Exiting due to an error"
}
workflow {
testError()
}There was a problem hiding this comment.
Awesome explanation! Thanks for going through that!
Now do you want to PR it to the official Nextflow docs or Nextflow gotchas? 😁
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Haha, there's always a catch. Not quite sure if there's an obvious place in the Nextflow docs. Maybe a good home would be the "Groovy imports" module in the advanced training which is currently being merged into training.nextflow.io.
Merged
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This PR makes it possible to skip MultiQC when running the pipeline.
Additionally, it also fixes error raising (e.g. before, a missing column in the input samplesheet would result in
No such variable: Nextflowinstead of the correct error message).PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.