search

nextflow-io / patterns

A curated collection of Nextflow implementation patterns
http://nextflow-io.github.io/patterns/
MIT License
329 stars 72 forks source link

blast-parallel.nf adding makeblastdb process #5

Closed mictadlo closed 6 years ago

mictadlo commented 7 years ago

Hi, Would you be able to add makeblastdb process to blast-parallel.nf?

genomes = Channel.fromPath(params.genomes)

process formatBlastDatabases {

  storeDir '/db/genomes'

  input:
  file species from genomes

  output:
  file "${dbName}.*" into blastDb

  script:
  dbName = species.baseName
  """
  makeblastdb -dbtype nucl -in ${species} -out ${dbName}
  """
}

Thank you in advance.

Michal

pditommaso commented 6 years ago

Sorry, I've seen this only now. Is this still an open issue ?

mictadlo commented 6 years ago

Yes, it is.

mictadlo commented 6 years ago

Unfortunately, I still do not know how to combine makeblastdb and blast with nextflow together. Is there any HOWTO?

pditommaso commented 6 years ago

Please post the question in the discussion forum.

Lcornet commented 5 years ago

Hi,

Same issue, did you find a solution? I don't find the discussion in the forum.

mictadlo commented 4 years ago

No, I didn't, and I forgot to post it to the forum. Maybe do you want to post it?