Add samplesheet examples #82
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adamrtalbot
commented
Jul 26, 2023
adamrtalbot
commented
- Changes samplesheet examples to start simple and build up
- Moves splitting example to middle region
- Tries to harmonise examples to use the same or similar channels. This idea should be taken further.
- Changes samplesheet examples to start simple and build up - Moves splitting example to middle region - Tries to harmonise examples to use the same or similar channels. This idea should be taken further.
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Relates to #81 |
| Might create the channel: | ||
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| ```nextflow | ||
| tuple val(meta), path(fastq_1), path(fastq_2), path(bed) |
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I'm not entirely convinced this is the cleanest and most clear way of representing the channel structure, maybe something like [meta, fastq_1.fastq, fastq_2.fastq, sample1.bed] will be more clear for beginners?
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I've tried to match an input/output declaration for a process. Perhaps I could include both. What does the .fastq or .bed mean in your example?
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It was to emulate a filename, but yeah this is just a matter of representation. I'm not sure which way is the best or most clear to beginners. (although both should be fine I think)
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Take a look now, I've added a clarifying statement about what the channel is and how you would use it.
docs/samplesheets/examples.md
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| // Resulting in: | ||
| [ [ id: "sample" ], fastq1.R1.fq.gz, fastq1.R2.fq.gz, sample1.bed] | ||
| [ [ id: "sample2" ], fastq2.R1.fq.gz, fastq2.R2.fq.gz, null ] // A missing value from the samplesheet is null |
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| [ [ id: "sample2" ], fastq2.R1.fq.gz, fastq2.R2.fq.gz, null ] // A missing value from the samplesheet is null | |
| [ [ id: "sample2" ], fastq2.R1.fq.gz, fastq2.R2.fq.gz, [] ] // A missing value from the samplesheet is `[]` |
Files will default to [] when they aren't given (null will cause errors in processes where the files are used)
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One update worth reviewing - I've added an introduction and glossary section to the top. |
Nice addition! Thanks for contributing :p Let me know when you are fully ready with this so I can merge it |
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One last thing I'm unsure about - should we harmonise so all examples use the same example channel(s)? That way it's more consistent. |
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That's a good idea! Although we probably won't be able to apply everything logically on the fastq input channel here, but could be good for the examples that it does make sense for |
docs/samplesheets/examples.md
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| [ [ id: "sample2" ], fastq2.R1.fq.gz, fastq2.R2.fq.gz, [] ] // A missing value from the samplesheet is an empty list | ||
| ``` | ||
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| This could be used in the Nextflow process as: |
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This sentence sounds a bit confusing to me, as I would expect seeing the use of the channel instead of the process input declaration. Could we rephrase with something like "This channel can be used as input of a process where the input declaration is:"
Co-authored-by: Júlia Mir Pedrol <[email protected]>
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@mirpedrol @nvnieuwk I don't have permission to merge so I'll need one of you to close this PR. |
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Thank you @adamrtalbot! |
