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Using zcat for gzipped files is unnecessary for concatenation #339

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jfy133 opened this issue Jan 29, 2020 · 1 comment
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Using zcat for gzipped files is unnecessary for concatenation #339

jfy133 opened this issue Jan 29, 2020 · 1 comment
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enhancement New feature or request good first issue Good for newcomers
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V2.1 "Ravensburg"

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jfy133 commented Jan 29, 2020

Describe the bug
@lindenb pointed out we are currently using zcat to combine FASTQ files in AdapterRemoval. This is unncessary and can just use standard cat

We should remove all unncessary zcat for performance improvements!
@jfy133 jfy133 added the enhancement New feature or request label Jan 29, 2020
@jfy133 jfy133 added this to the V2.1 "Ulm" milestone Jan 29, 2020
@jfy133 jfy133 self-assigned this Jan 29, 2020
@jfy133 jfy133 added the good first issue Good for newcomers label Jan 29, 2020
@jfy133 jfy133 changed the title Using zcat for gzip files is unnecessary Using zcat for gzipped files is unnecessary for concatenation Jan 29, 2020
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jfy133 commented Jan 29, 2020

https://github.com/jfy133/eager/tree/zcat_to_cat

But

  1. Need to check output looks correct
  2. Lots of linting errors due to major nf-core tools update

So will take a bit longer

@jfy133 jfy133 mentioned this issue Jan 31, 2020
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@jfy133 jfy133 closed this as completed Feb 10, 2020
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