Differing numbers of rows error

Question

Differing numbers of rows error

Closed this issue 7 months ago · 4 comments

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Answer 1 · 2024-04-09T18:24:13.000Z

tl;dr leaving it for now - until someone has the time to fix

This happens when we call rcromwell::cromwell_workflow and what's returned from the fxn is a list where it can't easily be converted into a data.frame. We're doing a bunch of processing on the data returned from the Cromwell API in the rcromwell::cromwell_workflow function (See https://github.com/getwilds/rcromwell/blob/main/R/cromwellWorkflow.R) so perhaps it should be handled there - that is, cleaning up the output from the fxn so it's always a tibble and not a list sometimes

Answer 2 · 2024-04-09T19:05:18.000Z

Here's a screenshot.

Answer 3 · 2024-08-07T18:51:41.000Z

Looking at this now. The problem we're faced with is that inputs object in the output from gathering metadata on a single workflow can be shaped in many, many different ways. Currently in the shiny app we're trying to show inputs as a table/data.frame. I'm not sure we can show a meaningful representation of inputs as a table since we'd have to force a bunch of metadata that aren't related to each other into the same rows.

Asking in slack what folks think

Here's 3 examples of the variation in shapes

:p lobstr::tree(jsonlite::fromJSON(all_inputs[[1]]))
<list>
├─Panel_BWA_GATK4_Annovar.referenceGenome: <list>
│ ├─annovarDIR: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─annovar_operation: "g,f,f,f,f,f,f,f,f"
│ ├─annovar_protocols: "refGene,knownGene,dbnsfp35c,cosm..."
│ ├─dbSNP_vcf: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─dbSNP_vcf_index: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─known_indels_sites_VCFs<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
│ ├─known_indels_sites_indices<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
│ ├─ref_alt: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_amb: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_ann: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_bwt: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_dict: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_fasta: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_fasta_index: "/fh/fast/paguirigan_a/pub/Refere..."
│ ├─ref_name: "hg38"
│ ├─ref_pac: "/fh/fast/paguirigan_a/pub/Refere..."
│ └─ref_sa: "/fh/fast/paguirigan_a/pub/Refere..."
└─Panel_BWA_GATK4_Annovar.sampleBatch: S3<data.frame>
  ├─bamFile<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
  ├─bedFile<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
  └─sample_name<chr [2]>: "tumor", "normal"

:p lobstr::tree(jsonlite::fromJSON(all_inputs[[3]]))
<list>
└─parseBatchFile.batchFile: "/fh/fast/paguirigan_a/pub/Refere..."

:p lobstr::tree(jsonlite::fromJSON(all_inputs[[5]]))
<list>
├─SCG_10x_AML_Genotyping.STARgenome10Xdir: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.af_only_gnomad: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.af_only_gnomad_index: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.annovarDIR: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.annovar_operation: "g,f"
├─SCG_10x_AML_Genotyping.annovar_protocols: "refGene,knownGene"
├─SCG_10x_AML_Genotyping.barcodeConsensusScript: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.batchOfSamples: S3<data.frame>
│ ├─R1FastqEnriched: <list>
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ └─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ ├─R1FastqsGEX: <list>
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ └─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ ├─R2FastqEnriched: <list>
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ ├─"s3://fh-pi-paguirigan-a-eco/tg/S..."
│ │ └─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ ├─R2FastqsGEX: <list>
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ ├─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ │ └─<chr [2]>"s3://fh-pi-p...", "s3://fh-pi-p..."
│ ├─bulkVCF<chr [7]>: "s3://fh-pi-p...", "s3://fh-pi-p...", "s3://fh-pi-p...", "s3://fh-pi-p...", "s3://fh-pi-p...", "s3://fh-pi-p...", "s3://fh-pi-p..."
│ ├─cellNumber<chr [7]>: "8000", "8000", "8000", "8000", "8000", "9000", "8000"
│ ├─cellrangerSample<chr [7]>: "Mix-5050-1-G...", "RO50292-GEX", "OCI-AML3-MOL...", "Mix-5050-2-G...", "MOLM14-L1-GE...", "OCI-AML3-GEX...", "AML3102-GEX"
│ ├─cellrangerSampleENR<chr [7]>: "Mix-5050-1-E...", "RO50292-EN", "OCI-AML3-MOL...", "Mix-5050-2-E...", "MOLM14-L1-EN...", "OCI-AML3-EN-...", "AML3102-EN"
│ ├─molecular_id<chr [7]>: "M00002390", "M00002392", "ClonalMix1", "M00002391", "M00002389", "M00002388", "AML3102"
│ ├─sampleNamexxxxxxx<chr [7]>: "Mix-5050-1", "NA", "NA", "NA", "NA", "NA", "NA"
│ └─sampleName<chr [7]>: "NA", "RO50292", "OCI-AML3-MOL...", "Mix-5050-2", "MOLM14-L1", "OCI-AML3", "AML3102"
├─SCG_10x_AML_Genotyping.bedfileforTarget: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.cellRangerReferenceDir: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.dbSNP_vcf: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.dbSNP_vcf_index: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.hotspotBed: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.intervalListforTarget: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.known_indels_sites_VCFs<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
├─SCG_10x_AML_Genotyping.known_indels_sites_indices<chr [2]>: "/fh/fast/pag...", "/fh/fast/pag..."
├─SCG_10x_AML_Genotyping.ref_dict: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.ref_fasta: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.ref_fasta_index: "/fh/fast/paguirigan_a/pub/Refere..."
├─SCG_10x_AML_Genotyping.ref_name: "hg38"
└─SCG_10x_AML_Genotyping.referenceGenome: "GRCh38.gencode.v31"

Answer 4 · 2024-08-08T19:05:28.000Z

After discussion in slack decided that

at least some people do have a need for VIEWING this data in the app (vs. just clicking to copy/paste in a text editor outside the app)
we'd test out some options for viewing the data in the app
- https://github.com/timelyportfolio/listviewer via Dan
- others?
if the viewing actual data options don't work then just provide a download button