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fastq-dump parallel error in tutorial #58

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Koen-vdl opened this issue Aug 12, 2021 · 1 comment
Open

fastq-dump parallel error in tutorial #58

Koen-vdl opened this issue Aug 12, 2021 · 1 comment

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@Koen-vdl
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Koen-vdl commented Aug 12, 2021

Thanks for this great resource. fastqc-dump is fairly poorly documented so this workbook was a great starting point for me.

I think there is a small error on: https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0

parallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: SRR.numbers

I believe this will only work if you cat SRR.numbers

parallel --jobs 3 "fastq-dump --split-files --origfmt --gzip {}" ::: $( cat SRR.numbers)

@molecules
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molecules commented Nov 24, 2021

Yes, $( cat SRR.numbers) would work, or you can use four colons instead of three (as just now suggested in pull request #60).

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