vcfMerger parsing sample names

[tgenahmet]

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]

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.

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-- *Austin Christofferson* Bioinformatician Translational Genomics Research Institute 445 North Fifth Street, Phoenix, AZ 85004 (W) 602-343-8671 | (M) 480-650-4067 achristofferson@tgen.org | www.keatslab.org | www.tgen.org 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> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALdsNmeo2enO53X-bgmJsZ5mHav0VBADks5rlFz4gaJpZM4MarH4> .

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[tgenahmet]

config file validation now makes sure no periods are used.