We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Dear all,
bcbio-vm does not seem to support minimap2, even thought bcbio-nextgen does:
bcbio-vm
minimap2
bcbio-nextgen
bcbio_vm.py install --cores 30 --tools --data --genomes hg19 --genomes hg38 --aligners bwa --aligners minimap2 --aligners star --aligners hisat2 usage: bcbio_vm.py install [-h] [--genomes {GRCh37,hg19,hg38,hg38-noalt,mm10,mm9,rn6,rn5,canFam3,dm3,galGal4,phix,pseudomonas_aeruginosa_ucbpp_pa14,sacCer3,TAIR10,WBcel235,xenTro3,Zv9,GRCz10}] [--aligners {bowtie,bowtie2,bwa,novoalign,rtg,snap,star,ucsc,seq,hisat2}] [--datatarget {variation,rnaseq,smallrna,gemini,cadd,vep,dbnsfp,battenberg,kraken}] [--data] [--tools] [--wrapper] [--image IMAGE] [--cores CORES] bcbio_vm.py install: error: argument --aligners: invalid choice: 'minimap2' (choose from 'bowtie', 'bowtie2', 'bwa', 'novoalign', 'rtg', 'snap', 'star', 'ucsc', 'seq', 'hisat2')
Is this intended? best,
The text was updated successfully, but these errors were encountered:
No branches or pull requests
Dear all,
bcbio-vm
does not seem to supportminimap2
, even thoughtbcbio-nextgen
does:Is this intended?
best,
The text was updated successfully, but these errors were encountered: