Interface for read mappers?

[sdwfrost]

I've doing some work on read mapping of viral sequences, and to add value, I'd like to build Bioboxes for read mappers such as SMALT, NextGenMap etc. How does one propose a format to have something like:

docker pull bioboxes/smalt

biobox run \
  read_mapper \
  bioboxes/smalt \
  --input reads.fq \
  --reference ref.fa \
  --output alignment.bam

Is there a convention for the flags for paired end read files as well as how to use program-specific flags?

[pbelmann]

Hi Simon,

How does one propose a format

the first step would be to create an rfc like this one: https://github.com/bioboxes/rfc/blob/master/container/short-read-assembler/rfc.mkd

If you could create a pull request with an rfc, we would implement the command line interface for the biobox command line python tool.

[...] how to use program-specific flags?

Program specific flags are listed in a file like this one here .

A task like "default" or "careful" would be specified after the image name:

biobox run \
  read_mapper \
  bioboxes/smalt \
  default \
  --input reads.fq \
  --reference ref.fa \
  --output alignment.bam

Is there a convention for the flags for paired end read files [...]

In case of the short read assembler interface we simply stated in the biobox.yaml whether the input is single end or paired end as you can see here

[pbelmann]

@sdwfrost If you still interested in a read mapping interface for bioboxes, please reopen this issue. We would be glad, to help you with this.