deepvariant
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nf-core
Please consider using/contributing to https://github.com/nf-core/sarek
This PR introduces a breaking change and modernizes the pipeline to rely upon `DSL2` of Nextflow along with the latest `nf-core` community guidelines.
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...
I'm getting an error when trying to pull with singularity (version 3.5.2-1.el7) ``` singularity pull --name nf-core-deepvariant.simg shub://nf-core/deepvariant FATAL: While pulling shub image: failed to get manifest for: shub://nf-core/deepvariant: the...
Currently, the pipeline uses "*.bam" to find input files. We have, for a while now, switched to CRAM since the space savings are significant (50%). Any chance that the pipeline...
Please add support for centralized configs soon: https://github.com/nf-core/configs
@ewels Hello, 1) Could you update the pipeline to 0.72 version? 2) If i run it locally on my pc, will it use my acceleration cores of my GPU?
I want to analyse all the regions of genome.
Would be good to add the Zenodo DOI for the release to the main README of the pipeline in order to make it citable. You will have to do this...
Hello, I am attempting to install this pipeline using Singularity and run the test profile as follows, `nextflow run nf-core/deepvariant -profile test,singularity ` and am receiving the following error: `...
Hello, I've recently started using this pipeline for a project I'm working on and I've run into an issue. I ran one fasta file, one bam file and its corresponding...
