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MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
43 stars 19 forks source link

write-config #16

Closed blondie5125 closed 6 years ago

blondie5125 commented 6 years ago

Hello, I am currently working through your pipeline for future projects and am running into a problem when I try to configure the bam_pipeline. "--write-config" does not seem to work in configuring the pipeline, and I've tried many other possible variations. Every time I input "paleomix bam_pipeline --write-config", the output is just "BAM Pipeline v1.2.13.2" followed by "Usage", with the only possible commands following bam_pipeling being "help, example, makefile, dryrun, run and remap". How should I work around this?

Thank you so much,

Sarah

MikkelSchubert commented 6 years ago

Sorry for the trouble, but unfortunately the documentation was slightly wrong.

You need to add the "run" or "dryrun" sub-command before you can use the --write-config option. In other words, it should look like this: paleomix bam_pipeline run --write-config

And thank you for letting me know about this. I've updated the documentation with the correct usage.

Cheers, Mikkel

blondie5125 commented 6 years ago

Thank you Mikkel,

I got the pipeline to work for the tutorial, I appreciate the update and look forward to using it for my work.

Best,

Sarah

From: Mikkel Schubert notifications@github.com Sent: Wednesday, July 25, 2018 4:35:10 PM To: MikkelSchubert/paleomix Cc: Johnson, Sarah; Author Subject: [EXT] Re: [MikkelSchubert/paleomix] write-config (#16)

Sorry for the trouble, but unfortunately the documentation was slightly wrong.

You need to add the "run" or "dryrun" sub-command before you can use the --write-config option. In other words, it should look like this: paleomix bam_pipeline run --write-config

And thank you for letting me know about this. I've updated the documentation with the correct usage.

Cheers, Mikkel

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