allow meta tidiers for cohort data

umccr · Oct 25, 2024 · 5ea17ae · 5ea17ae
1 parent 42af0ed
commit 5ea17ae
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/R/meta_wgs_alignment_qc.R b/R/meta_wgs_alignment_qc.R
@@ -38,7 +38,7 @@ meta_wgs_alignment_qc <- function(pmeta, status = "Succeeded") {
       # output
       gds_outdir_dragen = purrr::map_chr(.data$output, list("dragen_alignment_output_directory", "location"), .default = NA),
       gds_outdir_multiqc = purrr::map_chr(.data$output, list("multiqc_output_directory", "location"), .default = NA),
-      SubjectID = sub("umccr__automated__wgs_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
+      SubjectID = sub("umccr__.*__wgs_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
     ) |>
     tidyr::separate_wider_delim(
       cols = "rgid", delim = ".",

diff --git a/R/meta_wts_alignment_qc.R b/R/meta_wts_alignment_qc.R
@@ -38,7 +38,7 @@ meta_wts_alignment_qc <- function(pmeta, status = "Succeeded") {
       # output
       gds_outdir_dragen = purrr::map_chr(.data$output, list("dragen_alignment_output_directory", "location"), .default = NA),
       gds_outdir_multiqc = purrr::map_chr(.data$output, list("multiqc_output_directory", "location"), .default = NA),
-      SubjectID = sub("umccr__automated__wts_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
+      SubjectID = sub("umccr__.*__wts_alignment_qc__(SBJ.*)__L.*", "\\1", .data$wfr_name),
     ) |>
     tidyr::separate_wider_delim(
       cols = "rgid", delim = ".",

diff --git a/R/meta_wts_tumor_only.R b/R/meta_wts_tumor_only.R
@@ -37,7 +37,7 @@ meta_wts_tumor_only <- function(pmeta, status = "Succeeded") {
       gds_outdir_multiqc = purrr::map_chr(.data$output, list("multiqc_output_directory", "location"), .default = NA),
       gds_outdir_arriba = purrr::map_chr(.data$output, list("arriba_output_directory", "location"), .default = NA),
       gds_outdir_qualimap = purrr::map_chr(.data$output, list("qualimap_output_directory", "location"), .default = NA),
-      SubjectID = sub("umccr__automated__wts_tumor_only__(SBJ.*)__L.*", "\\1", .data$wfr_name)
+      SubjectID = sub("umccr__.*__wts_tumor_only__(SBJ.*)__L.*", "\\1", .data$wfr_name)
     )
   d |>
     dplyr::select(