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Update to new workflow #8

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averagehat opened this issue Aug 7, 2015 · 2 comments
Open

Update to new workflow #8

averagehat opened this issue Aug 7, 2015 · 2 comments

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@averagehat
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We want to output a simple table of samplename, sampleid that can be loaded into Excel rather than a full samplesheet.
@averagehat
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Somewhat relevant
https://github.com/genomika/biotools/blob/cb87192579e2057443b765ab7834aa734aba347b/illumina/prepare_sample_sheet.py

@averagehat
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New workflow:

CSVScript, before run:
-> returns: new excel file with sampleid & smaplename = issue ids

  • creates: run issue + sample issues
    Lab tech uses new excel file to create run & samplesheet normally
    Machine runs, dumping output to VD_Research/TMPOUT

Sync Script, when run is finished:
Poll or manually run sync script with run folder & run issue #3
sync samples from TMPOUT as in miseq_sync.sync

?Link issue & run folder via samplesheet & issue xls file?

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@averagehat