Update usage.md for igenomes warning #1073
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Looks good to me, except that |
drpatelh
reviewed
Aug 31, 2023
docs/usage.md
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| - The igenomes file usage triggered by this option is outdated with respect to gene annotations. This can be particularly problematic for RNA-seq analysis, which relies on accurate gene annotation. | ||
| - Some iGenomes references (e.g., GRCh38) point to annotation files that use gene symbols as the primary identifier. This can cause issues for downstream analysis, such as the nf-core [differential abundance workflow](https://nf-co.re/differentialabundance) workflow. | ||
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| We recommend that you provide reference files directly, via `--gtf` and `--fasta`, and that supplied GTF files do not use gene names as `gene_id`. |
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Probably also worth extending these to provide genome indices too. And maybe even docs and commands to download via Ensembl. I am manually sharing them right now on Slack which isn't ideal.
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@drpatelh I've added the example download commands, and reworked a bit to make the existing discussion of indices more prominent.
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@nf-core-bot fix linting |
maxulysse
reviewed
Sep 4, 2023
| --input <SAMPLESHEET> \ | ||
| --outdir <OUTDIR> \ | ||
| --gtf <GTF> \ | ||
| --fasta <GENOME FASTA> \ |
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don't we need --igenomes_ignore --genome null too?
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... actually, could I be more provocative and suggest we lose --igenomes_ignore in favour of a new --load_igenomes? So non-use of iGenomes becomes the default position (since it's what we're recommending)?
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(realise I've broken the tests, I'll fix things up if folk agree this is the right way to go)
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What does --ignomes_ignore do specifically? I can see the use if there is no valid igenomes.config, but not otherwise. I just run with with --fasta and gtf and don't specify --genome at all (is that equivalent to --igenomes null?), and that works great (I do have igenomes_base in my profile).
Also, is there anything in iGenomes (QC references, etc.?) that is being used by default, even when --fasta and --gtf are provided? I suspect not, because when I don't specify the --genome I don't seem to be missing anything. If that is in fact the case, I am totally fine with not using iGenomes by default.
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What does
--ignomes_ignoredo specifically?
Literally just that conditional around the config load I think. The help in the schema says "Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config." - so clearly someone has encountered clashes of some sort in the past.
maxulysse
reviewed
Sep 5, 2023
drpatelh
approved these changes
Oct 13, 2023
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Thanks @pinin4fjords @tdanhorn! Will merge this and make any changes in a follow up PR. Due to the extensive changes it will be easier for me to update bits and bobs.
| @@ -23,6 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements | |||
| - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9 | |||
| - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation | |||
| - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module | |||
| - [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome | |||
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Suggested change
| - [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome | |
| - [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage usage of `--genome` |
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iGenomes are a pain:
So I propose some strong wording to advocate for supplying
--gtfand--fasta.Edit: file downloads added after feedback. I also tidied up the discussion of reference index handling that I thought had gotten a bit wordy, hope I haven't been too brutal.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).