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Skip later steps when no alignment is found #29

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charles-plessy opened this issue Dec 19, 2024 · 0 comments
Open

Skip later steps when no alignment is found #29

charles-plessy opened this issue Dec 19, 2024 · 0 comments
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enhancement New feature or request
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@charles-plessy
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Description of feature

I saw this in another pipeline

  //CheckM2 returns exit code 1 when Diamond doesn't find any hits
    withName: CHECKM2_PREDICT {
        errorStrategy = { task.exitStatus in (130..145) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
    }

Here we could do the same by making the lastal module exit with a given status when no alignment is found (which can be infered from the alignment statistics).

This probably requires to modify the module's source in the nf-core/modules repository, but I open this issue to keep track of the idea.

@charles-plessy charles-plessy added the enhancement New feature or request label Dec 19, 2024
@charles-plessy charles-plessy added this to the 2.0.0 milestone Dec 19, 2024
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