TSO500 ctDNA v1 refactor

[pdiakumis]

Refactoring cttso v1 support.

• Tidying is now workflow-based.
• Input is a GDS or local path to the Results folder, along with the Sample and Library IDs.
• Tidy tibbles now have more consistent structure and names with a name column and a data list-column. This enables complex files like the SampleAnalysisResults JSON to output multiple tidy tibbles (e.g. the sar_ tibbles below).

p <- file.path(
"gds://production/analysis_data/SBJ04651/tso_ctdna_tumor_only",
"20240223d1951163/L2400183/Results"
)
SampleID <- "PRJ230876"
LibraryID <- "L2400183"
prefix <- glue("{SampleID}__{LibraryID}")
t1 <- Wf_tso_ctdna_tumor_only$new(path = p, SampleID = SampleID, LibraryID = LibraryID)
d <- t1$download_files(max_files = 100, dryrun = F)
d_tidy <- t1$tidy_files(d)
d_write <- t1$write(
d_tidy,
outdir = file.path("my_outdir", "dracarys_tidy"),
prefix = prefix,
format = "tsv"
)

d_tidy |> print(n = 30)
# A tibble: 23 × 2
   name              data                 
   <chr>             <list>               
 1 acfc_maprg        <tibble [1 × 84]>    
 2 acfc_map          <tibble [1 × 86]>    
 3 acfc_trim         <tibble [1 × 37]>    
 4 acfc_cvg          <tibble [1 × 29]>    
 5 acfc_umistats     <tibble [1 × 31]>    
 6 acfc_umistatshist <tibble [162 × 3]>   
 7 acfc_svsum        <tibble [1 × 4]>     
 8 acfc_runtime      <tibble [1 × 9]>     
 9 targetcvg         <tibble [14 × 3]>    
10 fraglenhist       <tibble [39,026 × 2]>
11 msi               <tibble [1 × 6]>     
12 tmb               <tibble [1 × 8]>     
13 combinedvaro      <tibble [1,343 × 11]>
14 cnv               <tibble [59 × 11]>   
15 fusions           <tibble [0 × 3]>     
16 mergedsmallv      <tibble [1,341 × 21]>
17 sar_sampleinfo    <tibble [1 × 4]>     
18 sar_qc            <tibble [1 × 29]>    
19 sar_swconfds      <tibble [7 × 4]>     
20 sar_swconfother   <tibble [1 × 7]>     
21 sar_snv           <tibble [1,343 × 29]>
22 sar_cnv           <tibble [14 × 7]>    
23 tmbtrace          <tibble [1,529 × 20]>