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Merge pull request #181 from umccr/issues-180/cn
Handle zero CN gains/losses
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,133 @@ | ||
| # helpers for downloading S3 data for local testing | ||
| require(dracarys, include.only = "s3_list_files_dir") | ||
| require(dplyr) | ||
| require(rportal, include.only = "orca_query_url") | ||
| require(glue, include.only = "glue") | ||
| require(here, include.only = "here") | ||
| require(tibble, include.only = "tibble") | ||
| require(tidyr, include.only = "pivot_longer") | ||
|
|
||
| # make sure you have logged into AWS | ||
| c("AWS_ACCESS_KEY_ID", "AWS_SECRET_ACCESS_KEY", "AWS_REGION") |> | ||
| rportal::envvar_defined() |> | ||
| stopifnot() | ||
| token_orca <- rportal::orca_jwt() |> rportal::jwt_validate() | ||
| portalRunId <- "20241201d2c4e79d" # failed run | ||
|
|
||
| # query orca workflow manager for payload with rnasum s3 inputs | ||
| get_rnasum_inputs <- function(prid, token_orca) { | ||
| wfrid <- rportal::orca_prid2wfrid(prid = portalRunId, token = token) | ||
| states <- rportal::orca_wfrid2state(wfrid, token) # view states for gived wfrid | ||
| pldid <- states |> | ||
| filter(.data$status == "FAILED") |> | ||
| pull("payload") | ||
| url <- glue("https://workflow.prod.umccr.org/api/v1/payload/{pldid}") | ||
| pld <- rportal::orca_query_url(url, token) | ||
| s3inputs <- pld[["data"]][["inputs"]] |> | ||
| purrr::map(\(x) x |> stringr::str_replace("/$", "")) | ||
| return(s3inputs) | ||
| } | ||
|
|
||
| rnasum_inputs <- get_rnasum_inputs(portalRunId, token) | ||
| # patterns of files to fish out | ||
| rnasum_file_regex <- tibble::tribble( | ||
| ~regex, ~fun, | ||
| "quant\\.genes\\.sf$", "DragenWtsQuantGenesSfFile", | ||
| "quant\\.sf$", "DragenWtsQuantSfFile", | ||
| "fusion_candidates\\.final$", "DragenWtsFusionsFinalFile", | ||
| "fusions\\.pdf$", "ArribaFusionsPdfFile", | ||
| "fusions\\.tsv$", "ArribaFusionsTsvFile", | ||
| "somatic\\.pcgr\\.snvs_indels\\.tiers\\.tsv$", "PcgrTiersTsvFile", | ||
| "purple\\.cnv\\.gene\\.tsv$", "PurpleCnvGeneTsvFile", | ||
| "manta\\.tsv$", "MantaTsvFile", | ||
| "mapping_metrics\\.csv$", "MapMetricsFile" | ||
| ) | ||
| outdir <- here::here("nogit/patient_data") | ||
|
|
||
| # melt s3_indir columns to get a single column with paths to S3 directories | ||
| # of interest, and fish out files of interest from each of them, then download | ||
| meta_rnasum <- rnasum_inputs |> | ||
| tibble::as_tibble_row() |> | ||
| tidyr::pivot_longer(contains("Uri"), names_to = "folder_type", values_to = "s3_indir") |> | ||
| mutate(folder_type = sub("Uri$", "", .data$folder_type)) |> | ||
| select(subjectId, wtsTumorLibraryId, folder_type, s3_indir) |> | ||
| rowwise() |> | ||
| mutate( | ||
| down = list(dracarys::dr_s3_download(s3dir = s3_indir, outdir = outdir, max_objects = 1000, regexes = rnasum_file_regex, dryrun = F)) | ||
| ) |> | ||
| ungroup() | ||
|
|
||
| # saveRDS(meta_rnasum, here(glue("nogit/patient_data/down_{date1}.rds"))) | ||
| # meta_rnasum <- here::here(glue("nogit/patient_data/down_{date1}.rds")) |> readr::read_rds() | ||
| rnasum_params_set <- function(arriba_pdf, arriba_tsv, dataset, dragen_fusions, dragen_mapping_metrics, sv_tsv, | ||
| pcgr_tiers_tsv, purple_gene_tsv, report_dir, salmon, | ||
| sample_name, subject_id) { | ||
| params <- list( | ||
| arriba_pdf = arriba_pdf, | ||
| arriba_tsv = arriba_tsv, | ||
| batch_rm = TRUE, | ||
| cn_gain = 95, | ||
| cn_loss = 5, | ||
| dataset = dataset, | ||
| dataset_name_incl = FALSE, | ||
| dragen_fusions = dragen_fusions, | ||
| dragen_mapping_metrics = dragen_mapping_metrics, | ||
| drugs = FALSE, | ||
| filter = TRUE, | ||
| immunogram = FALSE, | ||
| log = TRUE, | ||
| sv_tsv = sv_tsv, | ||
| norm = "TMM", | ||
| pcgr_splice_vars = TRUE, | ||
| pcgr_tier = 4, | ||
| pcgr_tiers_tsv = pcgr_tiers_tsv, | ||
| project = "-", | ||
| purple_gene_tsv = purple_gene_tsv, | ||
| report_dir = report_dir, | ||
| salmon = salmon, | ||
| sample_name = sample_name, | ||
| sample_source = "-", | ||
| save_tables = TRUE, | ||
| scaling = "gene-wise", | ||
| subject_id = subject_id, | ||
| top_genes = 5, | ||
| transform = "CPM", | ||
| umccrise = NULL | ||
| ) | ||
| params | ||
| } | ||
|
|
||
| # now unmelt to have one row per run | ||
| d_runs <- meta_rnasum |> | ||
| tidyr::unnest(down) |> | ||
| dplyr::select(subjectId, libraryId = "wtsTumorLibraryId", type, localpath) |> | ||
| tidyr::pivot_wider(names_from = type, values_from = localpath) | ||
|
|
||
| # slice to whichever run you want from d | ||
| d_runs |> | ||
| # dplyr::slice(1) |> | ||
| dplyr::rowwise() |> | ||
| dplyr::mutate( | ||
| rnasum_dataset = "PANCAN", | ||
| params = list( | ||
| rnasum_params_set( | ||
| arriba_pdf = ArribaFusionsPdfFile, | ||
| arriba_tsv = ArribaFusionsTsvFile, | ||
| dataset = rnasum_dataset, | ||
| dragen_fusions = DragenWtsFusionsFinalFile, | ||
| dragen_mapping_metrics = MapMetricsFile, | ||
| sv_tsv = MantaTsvFile, | ||
| pcgr_tiers_tsv = PcgrTiersTsvFile, | ||
| purple_gene_tsv = PurpleCnvGeneTsvFile, | ||
| report_dir = here::here(glue::glue("nogit/patient_data/reports/{subjectId}_{libraryId}_{rnasum_dataset}")), | ||
| salmon = DragenWtsQuantGenesSfFile, | ||
| sample_name = glue::glue("{subjectId}_{libraryId}"), | ||
| subject_id = subjectId | ||
| ) | ||
| ), | ||
| rnasum_rmd = RNAsum::rnasum_rmd( | ||
| out_file = here::here(glue::glue("nogit/patient_data/reports_html/{subjectId}_{libraryId}_{rnasum_dataset}.html")), | ||
| quiet = FALSE, pars = params | ||
| ) | ||
| ) |> | ||
| dplyr::ungroup() |