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Extra clarifications for indices, FastP and general cleanup#136

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apeltzer merged 1 commit intodevfrom
help_message_improvements
Feb 1, 2019
Merged

Extra clarifications for indices, FastP and general cleanup#136
apeltzer merged 1 commit intodevfrom
help_message_improvements

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@jfy133 jfy133 commented Feb 1, 2019

General clarifications for index files (to sync with docs), FastP and general typo corrections and re-ordering.

Question for @apeltzer - what is the default bam_discard_unmapped output format? Should we set one?

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@jfy133 jfy133 requested a review from apeltzer February 1, 2019 11:29
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❤️ this :-)

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apeltzer commented Feb 1, 2019

There is no default case! If you specify the bam_discard_unmapped parameter, you will also need to specify what should be done with unmapped reads (bam, discard, fastq,both) or you end up having just quality filtered BAM files....

@apeltzer apeltzer merged commit df6305f into dev Feb 1, 2019
@jfy133 jfy133 deleted the help_message_improvements branch February 2, 2019 12:51
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jfy133 commented Feb 2, 2019

Is there an error though if you don't specify the type?

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apeltzer commented Feb 2, 2019

Not yet no - can make that happen

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