search

KevinMenden / hybrid-assembly

Pipeline for hybrid assembly using short and long reads.
MIT License
7 stars 5 forks source link

Path string cannot be empty Missing `fromPath` parameter #1

Closed sajjadasaf closed 3 years ago

sajjadasaf commented 3 years ago

I tried to use docker version but it shows the following error. Could you kindly help me to solve this.

Thank you

nextflow run kevinmenden/hybrid-assembly -profile docker --reads '/media/laptop/DBG2OLC-master/Pacbio.fasta' N E X T F L O W ~ version 20.10.0 Launching kevinmenden/hybrid-assembly [exotic_leakey] - revision: c2aef5f047 [master] Path string cannot be empty Missing fromPath parameter

KevinMenden commented 3 years ago

You'll need to specificy both short and long reads, as it is a hybrid-assembly pipeline. See this command:

nextflow run kevinmenden/hybrid-assembly --shortReads '*_R{1,2}.fastq.gz' --longReads long_reads.fastq.gz --assembler spades -profile docker

You find a better description in the docs https://github.com/KevinMenden/hybrid-assembly/blob/master/docs/usage.md

sajjadasaf commented 3 years ago

Thank you very much for your reply. problem solved. Thank you again for such a nice software.