Add RSEM #389
Add RSEM #389
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Merged the template already today, so if you wait for around 30 mins, at least the linting should be fine then... |
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Merge #394 first. |
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bin/scrape_software_versions.py
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| results['Qualimap'] = '<span style="color:#999999;\">N/A</span>' | ||
| results['MultiQC'] = '<span style="color:#999999;\">N/A</span>' | ||
| results["nf-core/rnaseq"] = '<span style="color:#999999;">N/A</span>' | ||
| results["Nextflow"] = '<span style="color:#999999;">N/A</span>' |
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@grst , I'm not sure that these editor-config i.e. ' to " related changes are necessary. Or perhaps we are adapting this as a convention throughout?
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We don't usually enforce this kind of thing (except for maybe tabs/spaces). I wrote this code originally I think and I prefer single quotes, everyone has their own preference 😉 Generally I think it's nicest to just stick with whatever is already there though, saves a massive diff and means the line history is fair.
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Though here it looks like the backslashes need removing in the span, so it doesn't really matter.
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Seems like I didn't pay attention to my black.
I agree that diffs should be minimal and will revert this (except for the superfluous backslashes I guess)
| * STEP 11 - Transcriptome quantification with Salmon | ||
| * STEP 15 - Transcriptome quantification with Salmon |
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This is a good idea to divide the codebase in steps, however, these tend to add maintainence as well and eventuallly become out of sync. Maybe we could start relying on NOTE or simply STEP for this purpose?
abhi18av
dismissed
their stale review
Better to wait for a more experienced reviewer
| skip_rsem = params.skip_rsem | ||
| if (!params.skipAlignment && !params.skip_rsem && params.aligner != "star") { | ||
| skip_rsem = true | ||
| println "RSEM only works with STAR. Disabling RSEM." |
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According to the release notes for RSEM 1.3.3 (https://deweylab.github.io/RSEM/updates.html) there is now a hisat option available.
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I wasn't aware of that. Would indeed be a nice addition.
However I won't have time to look into this any time soon.
Therefore, I opt for merging it now, and adding RSEM+Hisat support in a second PR.
This PR adds RSEM to the pipeline (Fixes #70).
Notes:
I downgradedsalmonto0.14.2because the env could not be resolved with1.0.0even before adding rsemLinting fails already for thedevbranch. I didn't attempt to fix it, but don't believe I introduce additional lint.PR checklist
devrather thanmasternextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md