diff --git a/inst/rmd/umccr_portal/portal_summary.Rmd b/inst/rmd/umccr_portal/portal_summary.Rmd index 02033cf..36b0d77 100644 --- a/inst/rmd/umccr_portal/portal_summary.Rmd +++ b/inst/rmd/umccr_portal/portal_summary.Rmd @@ -116,8 +116,8 @@ get_sbj_url <- function(x, colour = NULL, account = "pro") { # Get metadata for workflows run within the date range # options(width = 150) fmt1 <- "%Y-%m-%dT%H:%M:%S" -date_start <- as.POSIXct("2023-11-02T00:00:01", format = fmt1) -date_end <- as.POSIXct("2023-11-04T23:59:59", format = fmt1) +date_start <- as.POSIXct("2023-11-22T00:00:01", format = fmt1) +date_end <- as.POSIXct("2023-11-23T23:59:59", format = fmt1) wf_order <- c( "bcl_convert", "tso_ctdna_tumor_only", @@ -139,7 +139,7 @@ lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds")) # saveRDS(lims_raw, file = lims_rds) lims_raw <- readr::read_rds(lims_rds) pmeta_rds <- here(glue("nogit/data_portal/workflows/{as.Date(date_end)}.rds")) -# pmeta_raw <- dracarys::portal_meta_read(rows = 15, account = "prod") +# pmeta_raw <- dracarys::portal_meta_read(rows = 200, account = "prod") # saveRDS(pmeta_raw, file = pmeta_rds) pmeta_raw <- readr::read_rds(pmeta_rds) pmeta <- pmeta_raw |> @@ -302,7 +302,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_tso_ctdna_tumor_only(status = c("Succeeded", "Failed")) |> + dracarys::meta_tso_ctdna_tumor_only(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -332,7 +332,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_wgs_alignment_qc(status = c("Succeeded", "Failed")) |> + dracarys::meta_wgs_alignment_qc(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -362,7 +362,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_wts_alignment_qc(status = c("Succeeded", "Failed")) |> + dracarys::meta_wts_alignment_qc(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -392,7 +392,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_wts_tumor_only(status = c("Succeeded", "Failed")) |> + dracarys::meta_wts_tumor_only(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -422,7 +422,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_wgs_tumor_normal(status = c("Succeeded", "Failed")) |> + dracarys::meta_wgs_tumor_normal(status = c("Succeeded", "Failed", "Running")) |> tidyr::unite("SampleID__LibraryID___normal", SampleID_normal, LibraryID_normal, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor", SampleID_tumor, LibraryID_tumor, sep = "__") |> tidyr::pivot_longer(c("SampleID__LibraryID___normal", "SampleID__LibraryID___tumor"), names_to = c(NA, "Phenotype"), names_sep = "___", values_to = "SampleID__LibraryID") |> @@ -447,7 +447,7 @@ pmeta |> wf <- "umccrise" ``` -### 7. `r wf` +### 7. `r wf` {.active} ```{r} if (!chunks1[[wf]]) { @@ -457,7 +457,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_umccrise(status = c("Succeeded", "Failed")) |> + dracarys::meta_umccrise(status = c("Succeeded", "Failed", "Running")) |> tidyr::unite("SampleID__LibraryID___normal", SampleID_normal, LibraryID_normal, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor", SampleID_tumor, LibraryID_tumor, sep = "__") |> tidyr::pivot_longer(c("SampleID__LibraryID___normal", "SampleID__LibraryID___tumor"), names_to = c(NA, "Phenotype"), names_sep = "___", values_to = "SampleID__LibraryID") |> @@ -492,7 +492,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_rnasum(status = c("Succeeded", "Failed")) |> + dracarys::meta_rnasum(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -522,7 +522,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_star_alignment(status = c("Succeeded", "Failed")) |> + dracarys::meta_star_alignment(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -552,7 +552,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_oncoanalyser_wts(status = c("Succeeded", "Failed")) |> + dracarys::meta_oncoanalyser_wts(status = c("Succeeded", "Failed", "Running")) |> dplyr::left_join(lims, by = c("LibraryID", "SampleID", "SubjectID")) |> dplyr::left_join(clrs1 |> dplyr::select(sbjid, sbj_url), by = c("SubjectID" = "sbjid")) |> dplyr::mutate( @@ -583,7 +583,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_oncoanalyser_wgs(status = c("Succeeded", "Failed")) |> + dracarys::meta_oncoanalyser_wgs(status = c("Succeeded", "Failed", "Running")) |> tidyr::unite("SampleID__LibraryID___normal", SampleID_normal, LibraryID_normal, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor", SampleID_tumor, LibraryID_tumor, sep = "__") |> tidyr::pivot_longer(c("SampleID__LibraryID___normal", "SampleID__LibraryID___tumor"), names_to = c(NA, "Phenotype"), names_sep = "___", values_to = "SampleID__LibraryID") |> @@ -618,7 +618,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_oncoanalyser_wgts_existing_both(status = c("Succeeded", "Failed")) |> + dracarys::meta_oncoanalyser_wgts_existing_both(status = c("Succeeded", "Failed", "Running")) |> tidyr::unite("SampleID__LibraryID___normal___wgs", SampleID_normal_wgs, LibraryID_normal_wgs, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor___wgs", SampleID_tumor_wgs, LibraryID_tumor_wgs, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor___wts", SampleID_tumor_wts, LibraryID_tumor_wts, sep = "__") |> @@ -644,7 +644,7 @@ pmeta |> wf <- "sash" ``` -### 13. `r wf` {.active} +### 13. `r wf` ```{r} if (!chunks1[[wf]]) { @@ -654,7 +654,7 @@ if (!chunks1[[wf]]) { ```{r eval=chunks1[[wf]]} pmeta |> - dracarys::meta_sash(status = c("Succeeded", "Failed")) |> + dracarys::meta_sash(status = c("Succeeded", "Failed", "Running")) |> tidyr::unite("SampleID__LibraryID___normal", SampleID_normal, LibraryID_normal, sep = "__") |> tidyr::unite("SampleID__LibraryID___tumor", SampleID_tumor, LibraryID_tumor, sep = "__") |> tidyr::pivot_longer(c("SampleID__LibraryID___normal", "SampleID__LibraryID___tumor"), names_to = c(NA, "Phenotype"), names_sep = "___", values_to = "SampleID__LibraryID") |>