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ISUgenomics / bioinformatics-workbook

Bioinformatics Workbook repository
https://bioinformaticsworkbook.org
MIT License
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fastq-dump parallel error in tutorial #58

Open Koen-vdl opened 3 years ago

Koen-vdl commented 3 years ago

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 catSRR.numbers

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

molecules commented 2 years ago

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