Enhanced pipeline logic to support user-defined sample_name input
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…column based on 'sample' (meta.irida_id) for proper nf-iridanext plugin metadata functionality.
…s not provided in the samplesheet
…ted in the input samplesheet.
apetkau
requested changes
Aug 9, 2024
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Thanks so much @kylacochrane . This is amazing work. Looks great in IRIDA Next 😄
I have a few comments for you below. I will go through some more review of this next week.
emarinier
requested changes
Aug 12, 2024
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| // Ensure ID is unique by appending meta.irida_id if needed | ||
| while (processedIDs.contains(meta.id)) { | ||
| meta.id = "${meta.id}_${meta.irida_id}" | ||
| } |
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I think this is a useful solution to ensure unique keys, but I wonder if all of this is better serviced by unique keys with strict patterns (the same criteria as the previous IDs) handled by the schema_input.json code?
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I had an idea of about a different way of creating unique keys, so as to not rely on the meta.irida_id to append to meta.id.
The idea is, rather than appending meta.irida_id we append the index of the sample in the samplesheet.csv, so that every sample from {1..n} has _1 to _n appended.
My logic is that it might be less confusing to have _n for every sample rather than samples with that long IRIDA-Next ID appended to them. I'd suggest doing it to every sample, so users are not confused as to why it shows up. The code I was thinking would look something like this (my use of closures is amateur at best, so bear with me here).
Channel.fromSamplesheet("input").toList().flatMap { it.withIndex().collect{ entry, idx ->
entry[0].id = "${entry[0].id}_${idx}"
return [entry[0], entry[1], entry[2]]
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@emarinier thanks for the comment. The issue with unique keys/strict patterns is that the pipeline will then error if something is passed that is incorrect. Since IRIDA Next is pretty loose on sample names (e.g., allows spaces in names, etc) this could lead to errors in running those samples unless they were renamed
@sgsutcliffe thanks for your suggestion. I know we have already spoken about this for other pipelines/the best way forward.
sgsutcliffe
approved these changes
Aug 14, 2024
This was referenced Sep 9, 2024
sgsutcliffe
suggested changes
Sep 18, 2024
emarinier
approved these changes
Sep 18, 2024
This was referenced Sep 18, 2024
apetkau
requested changes
Sep 23, 2024
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Thanks so much @kylacochrane . This is amazing work 😄 . Sorry for taking so long to review it.
apetkau
requested changes
Sep 25, 2024
apetkau
approved these changes
Sep 25, 2024
sgsutcliffe
reviewed
Sep 25, 2024
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| ### `Changed` | ||
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| - Added the ability to include a `sample_name` column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration [PR24](https://github.com/phac-nml/speciesabundance/pull/24) |
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I added this to change descriptions (left it out originally but it was requested to be added). Basically create sub-bullet points with this information:
sample_namespecial characters will be replaced with"_"- If no
sample_nameis supplied in the columnsamplewill be used - To avoid repeat values for
sample_nameallsample_namevalues will be suffixed with the uniquesamplevalue from the input file
sgsutcliffe
reviewed
Sep 25, 2024
README.md
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| `sample_name`, allows more flexibility in naming output files or sample identification. Unlike `sample`, `sample_name` is not required to contain unique values. `Nextflow` requires unique sample names, and therefore in the instance of repeat `sample_names`, `sample` will be suffixed to any `sample_name`. Non-alphanumeric characters (excluding `_`,`-`,`.`) will be replaced with `"_"`. | ||
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| An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. |
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I would suggest putting this example samplesheet under the Input header than put tests/data/samplename_samplesheet.csv for the IRIDA-Next Optional Input Configuration, as this is the example samplesheet that shows the sample_name column the way you did in your docs/usage.
sgsutcliffe
reviewed
Sep 25, 2024
docs/usage.md
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| An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. | ||
| An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline, which includes the `sample_name` column. |
sgsutcliffe
approved these changes
Sep 25, 2024
Thanks for the suggestions Steven! I made the changes: 1af1a8f |
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For IRIDA Next Use
This PR enhances the pipeline configuration and logic, allowing users to specify a
sample_namefor their project samples in IRIDA Next. All output files generated by the pipeline will be named using the user-providedsample_nameinstead of the IRIDA Next Identifier.In IRIDA Next, each sample is automatically assigned an identifier by the platform. The changes in this PR ensure that the iridanext.output.json file is generated using this IRIDA Next Identifier (set to
meta.irida_idin the pipeline), guaranteeing that output files and metadata are accurately linked to the correct sample on the IRIDA Next platform.For local use, the pipeline includes logic to set
sample_nameequal tosample(i.e., meta.id = meta.irida_id), so local users don't need to provide both sample and sample_name in the input samplesheet.Additional logic is included to rename duplicates and deal with spaces in the
sample_nameparameter.This pipeline has been tested on a local instance of IRIDA Next, which has also been updated to support the additional
sample_nameparameter as detailed here: phac-nml/irida-next#678PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).