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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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Missing `fromPath` parameter #30

Open marcovth opened 3 years ago

marcovth commented 3 years ago

Hello ...

"fromPath" doesn't seem to be in the documentation for nf-core/deepvariant?

Thanks for suggestions.

nextflow run nf-core/deepvariant --fasta './Hg19ChrY.fa' --bam './VK446chrYx37.bam' --outdir './VK446Hg19ChrY_vcf' -profile singularity
N E X T F L O W  ~  version 20.04.1
Launching `nf-core/deepvariant` [adoring_minsky] - revision: 2b5486356c [master]
Missing `fromPath` parameter
apeltzer commented 3 years ago

This pipeline needs a lot of work to be useable again - @abhi18av agreed to give it a go, also see the #deepvariant channel on Slack for more info.

PhilPalmer commented 3 years ago

Hi @marcovth,

Sorry for the slight delay in response. I believe the issue is that you are not specifying a the --bed parameter for a BED file which is required by the pipeline.

The error message could be clearer though. This is the standard Nextflow error message when you try calling the fromPath operator on a variable that doesn't exist, here.

And agreed @apeltzer, the pipeline hasn't been updated in a couple of years now and so requires a lot of work to be updated