Improvements to Side Quest: Working with Files #744
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we don't need to title these code boxes, it's overkill
Will use this as a model for the others
Included a few TODO comments that are non-blocking for the PR, just ideas for future improvement
Still need to do the Summary section on scripting patterns but kid 2 wants me to play Roblox with her
…io/training into gvda-sidequests-layout
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Nextflow linting complete! ❌ 5 files had 33 errors 💡 Tip: Click filename locations to go directly to that code. View all 33 issues
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Fixes #700 |
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Nextflow linting complete! ❌ 5 files had 33 errors 💡 Tip: Click filename locations to go directly to that code. View all 33 issues
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vdauwera
changed the title
+ updated the solution + changed a few variable names etc to generalize (make less domain specific)
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Nextflow linting complete! ❌ 5 files had 33 errors 💡 Tip: Click filename locations to go directly to that code. View all 33 issues
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Contributor
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Nextflow linting complete! ❌ 5 files had 33 errors 💡 Tip: Click filename locations to go directly to that code. View all 33 issues
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| File name: patientA_rep1_normal_R1_001.fastq.gz | ||
| Simple name: patientA_rep1_normal_R1_001 | ||
| Extension: gz | ||
| Parent directory: /nextflow-io/training/blob/bb187e3bfdf4eec2c53b3b08d2b60fdd7003b763/side-quests/working_with_files/data |
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Here, and the next lines, are inaccurate. The original code probably used processes. I say this because without processes, the file is not staged and then the following explanations do not fit. One easy solution here would be to turn this snippet into a workflow with a process.
The correct output is: Parent directory: /nextflow-io/training/master/side-quests/working_with_files/data
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The difference is just pointing at a SHA vs pointing at a blob, but you're right, it should be consistent
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What SHA? The file is not downloaded.
mribeirodantas
requested changes
Dec 5, 2025
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We gotta fix the section 2 issue (the current explanation expects it to work as if it was within a process, but we are not using Nextflow processes there).
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The blob doesn't indicate it was used in a process, just the that the git link provided pointed at a specific SHA. |
pinin4fjords
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Dec 8, 2025
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Minor comments you can address, but giving a thumbs up to unblock you when you're ready to merge
| This is a mini-workflow (without any processes) that refers to a single file path in its workflow, then prints it to the console, along with its class. | ||
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| !!! note | ||
| <details> |
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Can't we use the mkdocs admonition? (??? etc?)
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| As advertised, this is a small workflow with one process (`COUNT_LINES`) that is meant to take a file input and count how many lines are in it. | ||
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| <details> |
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Can't we use the mkdocs admonition? (??? etc?)
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| input: | ||
| tuple val(meta), path(fastqs) | ||
| tuple val(meta), path( files) |
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| tuple val(meta), path( files) | |
| tuple val(meta), path(files) |
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| echo "Read 1: ${ files[0]}" >> ${meta.id}_stats.txt | ||
| echo "Read 2: ${ files[1]}" >> ${meta.id}_stats.txt |
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| echo "Read 1: ${ files[0]}" >> ${meta.id}_stats.txt | |
| echo "Read 2: ${ files[1]}" >> ${meta.id}_stats.txt | |
| echo "Read 1: ${files[0]}" >> ${meta.id}_stats.txt | |
| echo "Read 2: ${files[1]}" >> ${meta.id}_stats.txt |
| File name: patientA_rep1_normal_R1_001.fastq.gz | ||
| Simple name: patientA_rep1_normal_R1_001 | ||
| Extension: gz | ||
| Parent directory: /nextflow-io/training/blob/bb187e3bfdf4eec2c53b3b08d2b60fdd7003b763/side-quests/working_with_files/data |
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The difference is just pointing at a SHA vs pointing at a blob, but you're right, it should be consistent
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Not the blob. The "[...] current explanation [...]" indicates. |
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Improvements to the Working with Files Side Quest
Based on my experience teaching in Nov 2025
(Branch was started from my side quests layout improvements branch)