question: how to override mapper parameters?

karel-brinda / rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

http://karel-brinda.github.io/rnftools

MIT License

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Closed astewart-twist closed 7 years ago

astewart-twist commented 8 years ago

Is it possible somehow to pass parameters to the mapping algorithm, similar to how args can be passed to different read simulators?

For example:

alignments = [
    smbl.prog.BwaMem(
      fasta=reference,
      fastq_1=reads,
      bam="BWA-MEM.bam",
      params="-t 4 -E 0,1",
    ),
  ]

karel-brinda commented 8 years ago

Hello, it is not currently possible. If you need this feature, I can add it or you can make a pull request for it. However, I currently prefer to have separate Snakefiles and directories for read simulation, mapping, and evaluation. See, e.g., https://github.com/karel-brinda/dymas/tree/ococo/experiments/exp1.01__Borrelia__0.07-baq.

karel-brinda commented 7 years ago

Since the SMBL dependency has been removed from RNFtools, I am closing this issue.