fix annoying PRESEQ failure for methylseq

[maxulysse]

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
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[ewels]

Thank you!

[edmundmiller]

Shouldn't this be upstreamed to modules or this should have bumped the version?

[ewels]

Shouldn't this be upstreamed to modules

This is modules...? I don't understand.

I don't think that a version bump is required to add this flag.

[ewels]

I don't think that a version bump is required to add this flag.

Though it looks like 3.2.0 is available..

[edmundmiller]

This is modules...? I don't understand.

Don't mind me, saw methylseq in the title and misread it I guess 😅

[sateeshperi]

@maxulysse / @ewels why was the strategy changed from ignore to retry here ?

[edmundmiller]

Looks like it's still open nf-core/methylseq#161

[sateeshperi]

yes so, ignore makes sense....not sure why it was changed to retry in this PR

[maxulysse]

I think maybe ignore was too strict. I honestly don't remember...

[sateeshperi]

I think maybe because the intent was to retry with the defect mode with this line
args = task.attempt > 1 ? args.join(' -defects') : args // Disable testing for defects

[sateeshperi]

but, preseq still fails mostly in defect mode too and crashes the workflow. So, I would say ignore is better strategy.

It can either be here or I could set in methylseq base.config