Patch/nf anno utils #186
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Patch/nf anno utils #186
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This was
linked to
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Aug 15, 2024
anngvu
requested review from
ajs3nj,
jaybee84,
allaway,
cconrad8 and
aditya-nath-sage
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Hey, I'm annotating some RNAseq data now using this. One issue I came across in the vignette: |
allaway
reviewed
Sep 17, 2024
| #' @export | ||
| #' @return List `manifest` with manifests for each processed dataset, | ||
| #' and `sample_io` with linked inputs and outputs (should be used for provenance annotation). | ||
| processed_meta <- function(input, |
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processed_meta <- function(input,
This seemsl ike a bug:
> output <- map_sample_output_rnaseq(syn_out, fileview)
Path: Cutaneous Neurofibroma Data Resource/NF-OSI Processed Data/RNA-seq/processed
Found 66 files for STAR and Salmon
Found 0 files for featureCounts
Found 66 files for SAMtools
> meta <- processed_meta(input, output, workflow_link = wf_link)
Error in merge.data.table(output, input, by = "sample", all.x = TRUE, :
Elements listed in `by` must be valid column names in x and y
removing featureCounts from 'outputs' fixed the issue, so maybe this fct could just toss out empty results from the list?
allaway
reviewed
Sep 17, 2024
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| ```{r rnaseq-meta-submit, eval=FALSE} | ||
| annotate_with_manifest(manifest_1) |
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Suggested change
| annotate_with_manifest(manifest_1) | |
| annotate_with_manifest(manifest_1) |
I'm not sure what to put here as manifest_1 was not created earlier in the vignette. I tried these, which didn't work:
> annotate_with_manifest(meta)
Error in eval(jsub, SDenv, parent.frame()) : object 'entityId' not found
> annotate_with_manifest(meta$manifests)
Error in eval(jsub, SDenv, parent.frame()) : object 'entityId' not found
> annotate_with_manifest(meta$manifests$SAMtools)
Error in py_get_attr(x, name) :
AttributeError: 'Synapse' object has no attribute 'setAnnotations'. Did you mean: 'set_annotations'?
What am I missing? Thanks!
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Nevermind, I think this is a synapser version issue - oops.
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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.