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vcfMerger parsing sample names #17

Closed tgenahmet closed 7 years ago

tgenahmet commented 7 years ago

Can a sample name contain a period "."? I believe this is causing vcfMerger to parse file names incorrectly which in turn is creating a 0 byte vcf file which in turn is crashing GATK.

project: MMUM_008_N01502

I can't recall all of the sample name requirements for the pipeline... @denriquez @awchrist

awchrist commented 7 years ago

Nope. a period is not allowed. here is the power point that has the break down of the naming convention.

I’m guessing this was done outside of KBase? I can double check.

-- Austin Christofferson Bioinformatician Translational Genomics Research Institute

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From: tgenahmet notifications@github.com notifications@github.com Reply: tgen/pegasusPipe reply@reply.github.com reply@reply.github.com Date: March 12, 2017 at 2:00:41 PM To: tgen/pegasusPipe pegasuspipe@noreply.github.com pegasuspipe@noreply.github.com Cc: Austin Christofferson achristofferson@tgen.org achristofferson@tgen.org, Mention mention@noreply.github.com mention@noreply.github.com Subject: [tgen/pegasusPipe] vcfMerger parsing sample names (#17)

Can a sample name contain a period "."? I believe this is causing vcfMerger to parse file names incorrectly which in turn is creating a 0 byte vcf file which in turn is crashing GATK.

project: MMUM_008_N01502

I can't recall all of the sample name requirements for the pipeline... @denriquez https://github.com/denriquez @awchrist https://github.com/awchrist

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tgenahmet commented 7 years ago

config file validation now makes sure no periods are used.