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I would like to join #306

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cokelaer opened this Issue Dec 3, 2016 · 4 comments

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cokelaer commented Dec 3, 2016

Please, let us know if you would like to join the project.

You can contribute in various ways:

  • improving the documentation
  • add new Python functions / plotting
  • add new pipelines
  • add new docker images
  • add new visualisations
  • add HTML / Javascript functionalities
  • add bug reports

@cokelaer cokelaer added the question label Dec 3, 2016

@cokelaer cokelaer closed this Apr 27, 2017

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blaiseli Nov 30, 2017

Hi, I would like to join the project. I have written some snakemake pipelines, and I will try to see if they can be ported to the sequana infrastructure.

blaiseli commented Nov 30, 2017

Hi, I would like to join the project. I have written some snakemake pipelines, and I will try to see if they can be ported to the sequana infrastructure.

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cokelaer Nov 30, 2017

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I've added you. welcome on board.

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cokelaer commented Nov 30, 2017

I've added you. welcome on board.

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blaiseli Dec 6, 2017

To be honest, after having a quick look, it seems much more complicated than I expected. You seem to have implemented various layers of wrapping around snakemake. It looks like it requires quite some effort to become familiar enough with the whole infrastructure to be able to contribute.

I thought sequana was mostly a collection of plain snakemake pipelines or wrappers as described here: https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html

blaiseli commented Dec 6, 2017

To be honest, after having a quick look, it seems much more complicated than I expected. You seem to have implemented various layers of wrapping around snakemake. It looks like it requires quite some effort to become familiar enough with the whole infrastructure to be able to contribute.

I thought sequana was mostly a collection of plain snakemake pipelines or wrappers as described here: https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html

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cokelaer Dec 7, 2017

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@blaiseli we can discuss about if off line. In a few words, the wrapping around snakamake itself are actually rather small. We added a couple of functions to help users but they are optional. You can simply add your pipeline in a directory (sequana/pipelines) and that's it. You just need to add a README as explained in the developer guide. I think we enforce the use of a config file though and you must name your pipeline Snakefile.rules. I need to provide a complete documentation on this aspect.

However, if you want to decompose your pipelines with rules that can be re-used, then you will probably need to make a few updates to your code but then they can be re-used by other pipelines.

Again, we can discuss about this off-line.

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cokelaer commented Dec 7, 2017

@blaiseli we can discuss about if off line. In a few words, the wrapping around snakamake itself are actually rather small. We added a couple of functions to help users but they are optional. You can simply add your pipeline in a directory (sequana/pipelines) and that's it. You just need to add a README as explained in the developer guide. I think we enforce the use of a config file though and you must name your pipeline Snakefile.rules. I need to provide a complete documentation on this aspect.

However, if you want to decompose your pipelines with rules that can be re-used, then you will probably need to make a few updates to your code but then they can be re-used by other pipelines.

Again, we can discuss about this off-line.

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