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Patch/nf anno utils #186

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Patch/nf anno utils #186

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@anngvu anngvu commented Aug 15, 2024 •
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Closes #182, #183, #178 with substantial rewrite of nf annotation utils for processed data. Since the API has breaking changes, testers and anyone using the new version should refer to the updated vignette: https://github.com/nf-osi/nfportalutils/blob/patch/nf-anno-utils/vignettes/annotate-nf-processed-data.Rmd.

Update: since these changes are more complicated than usual, I'd only suggest Robert or Jineta do actual code review to spot bugs, everyone else is tagged for end-user awareness about the updated vignettes.

This was linked to issues Aug 15, 2024
nf-core output: add annotations for featureCounts files #178
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Fixes and enhancements for nf annotation utils #183
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@anngvu anngvu mentioned this pull request Sep 3, 2024
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allaway commented Sep 16, 2024

Hey, I'm annotating some RNAseq data now using this.

One issue I came across in the vignette:

> o <- map_sample_output_rnaseq(syn_out, fileview) # check outputs only
Path: A 3D Cutaneous Neurofibroma Model for Automated High-Throughput Drug Screenings/NFOSI-processed-data/NF-OSI Processing - Unreleased/RNA Sequencing/star_salmon
Found 3 files for STAR and Salmon
Error in strsplit(paths, "/") : non-character argument

@allaway allaway mentioned this pull request Sep 17, 2024
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@anngvu anngvu mentioned this pull request Nov 6, 2024
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@anngvu anngvu mentioned this pull request Nov 6, 2024
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@anngvu anngvu mentioned this pull request Nov 15, 2024
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