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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Allow users to start from intermediate steps #7

Closed abhi18av closed 3 years ago

abhi18av commented 3 years ago

Adding excerpts of discussion between @Mxrcon and @abhi18av

we can accept only the required file as input, or accept all the output files from other process, what do you think that works better? a more restrictive input or a more open that relies more on mtbseq to catch the input than nextflow.

I think that we could assume that the user would start from the first step of the workflow and reach the last, so we can focus only on that.

To facilitate the advanced use-case where people want to use the intermediate steps, maybe we can add another workflow which starts from like step-2 or step-3 just to show them how to stitch it together.

This would need to be explained in Readme.md.

abhi18av commented 3 years ago

Maybe, this might not be necessary since this becomes a bit didactic.

We have already wrapped all individual steps of mtbseq into NF processes/workflows and for advanced usage outlined in the issue description, advanced knowledge of NF is needed. Therefore, I think it might not be a good idea to overload the user with extra information.