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Improve documentation of config args to post processing scripts #55

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aineniamh opened this issue Jan 12, 2020 · 2 comments
Open

Improve documentation of config args to post processing scripts #55

aineniamh opened this issue Jan 12, 2020 · 2 comments
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enhancement New feature or request

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@aineniamh
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To allow binlorry to easily bin_by sample name, we need a column with that information, in addition to the barcode information already provided.

This only comes into play when you want to run multiple analyses at a time as currently the binlorry call uses the --filter_by flag and we sub in barcode and sample names at that point.

@aineniamh aineniamh added the enhancement New feature or request label Jan 12, 2020
@jameshadfield
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This information can (should) be provided by triggerPostProcessing to any downstream analysis tool such as binlorry. But it can't be stored in the annotation csv as RAMPART allows you to dynamically change the barcode - sample mapping via the UI (click the "config" icon).

@jameshadfield jameshadfield changed the title Annotations csv to include sample_name column Post processing scripts should have access to sample name - barcode maps Jan 13, 2020
@jameshadfield
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As of 1.1.0 this info is passed to binlorry via the snakemake config args sample_name=Kikwit barcodes=NB03 samples="{Kikwit: [NB03]}". Note that the UI can currently can only trigger them one sample at a time. Leaving this open as it needs documentation.

@jameshadfield jameshadfield changed the title Post processing scripts should have access to sample name - barcode maps Improve documentation of config args to post processing scripts Apr 1, 2020
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