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nf-core / deepvariant

Please consider using/contributing to https://github.com/nf-core/sarek
https://nf-co.re
MIT License
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Wrong results location in pipeline complete #15

Closed tarak77 closed 5 years ago

tarak77 commented 5 years ago

Hi, I was trying out the test pipeline mentioned in this repo, it runs fine 

=========================================
[warm up] executor > local
[b0/f25f59] Submitted process > get_software_versions
[8f/b18f3b] Submitted process > preprocess_bam (NA12878_S1.chr20.10_10p1mb.bam)
[af/6f2fe2] Submitted process > make_examples (NA12878_S1.chr20.10_10p1mb.bam)
[d5/ad6e27] Submitted process > call_variants (NA12878_S1.chr20.10_10p1mb.bam)
[7b/1cec4c] Submitted process > postprocess_variants (NA12878_S1.chr20.10_10p1mb.bam)
[nf-core/deepvariant] Pipeline Complete! You can find your results in /Users/tarakshisode/.nextflow/assets/nf-core/deepvariant/results

But for some reason I cannot find the results in that path. Any help?

apeltzer commented 5 years ago

This is a bug:

https://github.com/nf-core/deepvariant/blob/2b5486356c4dbd4dcb598b611281997119c2e350/main.nf#L516

Should be pointing simply to 

${params.outdir}

@PhilPalmer Can fix this I suppose :-)

For you, just use the second part of this suggestion:

./results

tarak77 commented 5 years ago

I see, thanks

PhilPalmer commented 5 years ago

Thanks, it's now changed on the dev branch