Timeline for Bash scripting FastQC for multiple fastq files in multiple directories
Current License: CC BY-SA 4.0
5 events
| when toggle format | what | by | license | comment | |
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| Oct 26, 2018 at 20:49 | comment | added | terdon♦ | heh, I know. Anyone who has spaces in fastq filenames deserves what they get :) sorry, I'm just very used to posting on Unix & Linux where this sort of detail is more relevant. | |
| Oct 26, 2018 at 19:30 | history | edited | conchoecia | CC BY-SA 4.0 |
made answer safe for whitespace in filenames.
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| Oct 26, 2018 at 19:28 | comment | added | conchoecia | whitespaces in file names. Oh, the horror! Thanks for your comments! | |
| Oct 26, 2018 at 17:18 | comment | added | terdon♦ |
+1, but note that this will break in the unlikely case where any of the fastq file names contain whitespace. A safer version is find . -name '*.fastq.gz' | awk '{printf("fastqc \"%s\"\n", $0)}' but that still fails in the (even more unlikely) case where a file name contains a newline. This should work for anything (but requires a version of find with -printf, like GNU find): find . -name '*.fastq.gz' -printf '"%p"\n' | parallel -j 25 --verbose.
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| Oct 26, 2018 at 17:02 | history | answered | conchoecia | CC BY-SA 4.0 |