Review and removal of redundancies #72
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Increase the image sizes of all images, as their content can be hard to read at the current sizes (small text size).
| <br> | ||
| <em>Example bioinformatics variant calling workflow/pipeline diagram from nf-core (https://nf-co.re/sarek) and simple RNA-Seq pipeline in DAG format. | ||
| </em> | ||
| <em> Example bioinformatics variant calling workflow/pipeline diagram from nf-core (https://nf-co.re/sarek) and simple RNA-Seq pipeline in DAG format. </em> |
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The caption doesn't match the diagram.
| 1. A `script` block that contains the bash commands ` printf '${read}` to print the name of the read file, and ` gunzip -c ${read} | wc -l` to count the number of lines in the gzipped read file. | ||
| We are now going to look at a sample Nextflow script that counts the number of | ||
| lines in a file. Create the file `word_count.nf` in the current directory using | ||
| your favourite text editor and copy-paste the following code: |
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This should be done with the live coding format in mind. No copy and paste. It's preferable to lead them through building up the script.
| /* Comments are uninterpreted text included with the script. | ||
| They are useful for describing complex parts of the workflow | ||
| or providing useful information such as workflow usage. | ||
| /* |
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It's important to keep the information on using comments.
As this is also live coded, I think comments should be kept simple, even though it's visually clearer to have ====== blocks.
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Maybe for the example script it doesn't matter, but I guess in practice one would likely just write the comment
Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
ggrimes
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Dec 8, 2023
Review and removal of redundancies
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