Lesson contribution grep #258
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Moved the division by four mention to the end of the "Redirecting output" section. Explained a potential issue caused by the default group separator, and used the recently introduced pipe to use fix it.
Included the -v '^--' edit in accordance to the previous commit to section 4. Added -h to avoid filenames in output and have "scripted_bad_reads.txt" ready to use with other tools e.g. fastqc in "Assessing Read Quality" from the "Data Wrangling and Processing for Genomics"
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Thank you @rortizmerino! This looks like a good solution to me. In addition, I think it will address #194 by giving a bit more context to redirection. What do you think @datacarpentry/shell-genomics-maintainers ? |
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Will merge this now. Thank you again @rortizmerino |
This was referenced Jan 31, 2020
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Made 2 commits including changes to the use of grep to get correctly formatted fastq files. The changes expand on the use of command redirection and use extended options for custom grep control. Changes are made in shell-genomics/04-redirection and shell-genomics/05-writing-scripts.
It is related to issue #224 , #232 , #227 , #230 , and maybe more so I guess is a hot topic, hope it helps.