Merge pull request #121 from umccr/tidy_update

Initial bcl_convert refactor

.Rbuildignore

@@ -24,7 +24,7 @@
 ^setup\.py$
 ^vignettes$
 inst/rmd/umccr_portal/html
-inst/rmd/umccr_workflows/alignment_qc/html
+inst/rmd/umccr_workflows/alignment_qc/nogit
 inst/rmd/umccr_workflows/bcl_convert/html
 inst/rmd/umccr_workflows/interop/html
 inst/rmd/umccr_workflows/umccrise/html

.github/workflows/conda_deploy.yaml

@@ -33,7 +33,7 @@ jobs:
         run: |
           dvc pull
           ls -l inst/extdata/*
-          conda mambabuild --R 4.2 ${recipe_path} -c conda-forge --token ${atoken}
+          conda mambabuild --R 4.3.3 ${recipe_path} -c conda-forge --token ${atoken}
       - name: 🔒 Conda lock
         run: |
           conda-lock lock --file ${env_yaml_path}/dracarys.yaml -p linux-64
@@ -99,7 +99,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: 🐳 Docker img build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           tags: ghcr.io/${{ github.repository }}:${{ env.VERSION }}
           context: . # yes, dot

DESCRIPTION

@@ -47,8 +47,8 @@ Imports:
     tibble,
     tidyr
 Suggests:
-    SparkR,
     rmarkdown,
+    SparkR,
     testthat (>= 3.0.0)
 Roxygen: list(markdown = TRUE,
               roclets = c("namespace", "rd", "roxytest::testthat_roclet"))

NAMESPACE

@@ -32,16 +32,15 @@ export(UmHrdetectTsvFile)
 export(UmQcSumFile)
 export(UmSigsSnvFile)
 export(VCMetricsFile)
+export(Wf)
+export(Wf_bcl_convert)
+export(Wf_tso_ctdna_tumor_only)
 export(WgsContigMeanCovFile)
 export(WgsCoverageMetricsFile)
 export(WgsFineHistFile)
 export(WgsHistFile)
 export(bcftools_parse_vcf)
 export(bcftools_parse_vcf_regions)
-export(bclconvert_read_adaptermetrics)
-export(bclconvert_read_demultiplexstats)
-export(bclconvert_read_indexhoppingcounts)
-export(bclconvert_read_topunknownbarcodes)
 export(date_log)
 export(dr_func_eval)
 export(dr_gds_download)
@@ -53,6 +52,7 @@ export(gds_file_download)
 export(gds_file_download_api)
 export(gds_file_presignedurl)
 export(gds_files_list)
+export(gds_files_list_fastq)
 export(gds_files_list_filter_relevant)
 export(gds_volumes_list)
 export(ica_token_validate)

R/Wf.R

@@ -0,0 +1,85 @@
+#' Workflow R6 Class
+#'
+#' @description Workflow is a base R6 class representing a bioinformatic
+#' workflow run from a UMCCR workflow manager.
+#'
+#' @examples
+#' p1 <- system.file("extdata/portaldb_workflow_top4.rds", package = "rportal") |>
+#'   readRDS() |>
+#'   dplyr::filter(type_name == "umccrise") |>
+#'   dplyr::slice(1)
+#' w <- Wf$new(
+#'   prid = p1$portal_run_id, type = p1$type_name, start = p1$start, end = p1$end,
+#'   status = p1$end_status, input = p1$input, output = p1$output
+#' )
+#' w
+#' @export
+Wf <- R6::R6Class(
+  "Wf",
+  public = list(
+    #' @field prid Portal run ID.
+    #' @field type Workflow type.
+    #' @field start Workflow start datetime.
+    #' @field end Workflow end datetime.
+    #' @field status Workflow end status.
+    #' @field input Workflow input JSON string.
+    #' @field output Workflow output JSON string.
+    prid = NULL,
+    type = NULL,
+    start = NULL,
+    end = NULL,
+    status = NULL,
+    input = NULL,
+    output = NULL,
+    #' @description Create a new Workflow object.
+    #' @param prid Portal run ID.
+    #' @param type Workflow type.
+    #' @param start Workflow start datetime.
+    #' @param end Workflow end datetime.
+    #' @param status Workflow end status.
+    #' @param input Workflow input JSON string.
+    #' @param output Workflow output JSON string.
+    initialize = function(prid = NULL, type = NULL, start = NULL, end = NULL,
+                          status = NULL, input = NULL, output = NULL) {
+      types <- c(
+        "bcl_convert",
+        "tso_ctdna_tumor_only",
+        "wgs_alignment_qc",
+        "wts_alignment_qc",
+        "wts_tumor_only",
+        "wgs_tumor_normal",
+        "umccrise",
+        "rnasum",
+        "star_alignment",
+        "oncoanalyser_wts",
+        "oncoanalyser_wgs",
+        "oncoanalyser_wgts_existing_both",
+        "sash"
+      )
+      assertthat::assert_that(
+        type %in% types
+      )
+      self$prid <- prid
+      self$type <- type
+      self$start <- start
+      self$end <- end
+      self$status <- status
+      self$input <- input
+      self$output <- output
+    },
+    #' @description Print details about the Workflow.
+    #' @param ... (ignored).
+    print = function(...) {
+      res <- tibble::tribble(
+        ~var, ~value,
+        "prid", self$prid,
+        "type", self$type,
+        "start", as.character(self$start),
+        "end", as.character(self$end),
+        "status", self$status,
+      )
+      print(res)
+      invisible(self)
+    }
+  ) # end public
+)