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portal summary: include Running status
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@pdiakumis
pdiakumis committed Nov 22, 2023
1 parent a77505f commit e904b13
Showing 1 changed file with 17 additions and 17 deletions.
34 changes: 17 additions & 17 deletions inst/rmd/umccr_portal/portal_summary.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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 |>
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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") |>
Expand All @@ -447,7 +447,7 @@ pmeta |>
wf <- "umccrise"
```

### 7. `r wf`
### 7. `r wf` {.active}

```{r}
if (!chunks1[[wf]]) {
Expand All @@ -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") |>
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down Expand Up @@ -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") |>
Expand Down Expand Up @@ -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 = "__") |>
Expand All @@ -644,7 +644,7 @@ pmeta |>
wf <- "sash"
```

### 13. `r wf` {.active}
### 13. `r wf`

```{r}
if (!chunks1[[wf]]) {
Expand All @@ -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") |>
Expand Down

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