diff --git a/R/ica.R b/R/ica.R index 84d44fa..73e2514 100644 --- a/R/ica.R +++ b/R/ica.R @@ -8,15 +8,16 @@ #' @param include Use PresignedUrl to include presigned URLs to all files within #' @param page_size Page size (def: 100). #' the GDS directory. +#' @param regexes Tibble with regex and function name. #' #' @return A tibble with type, bname, size, file_id, path, and presigned URL. #' @export -gds_files_list_filter_relevant <- function(gdsdir, token, pattern = NULL, include = NULL, page_size = 100) { +gds_files_list_filter_relevant <- function(gdsdir, token, pattern = NULL, include = NULL, page_size = 100, regexes = DR_FILE_REGEX) { pattern <- pattern %||% ".*" # keep all recognisable files by default cols_sel <- c("type", "bname", "size", "file_id", "path", "presigned_url") d <- dracarys::gds_files_list(gdsdir, token, include = include, page_size = page_size) |> dplyr::rowwise() |> - dplyr::mutate(type = purrr::map_chr(.data$bname, match_regex)) |> + dplyr::mutate(type = purrr::map_chr(.data$bname, \(x) match_regex(x, regexes))) |> dplyr::ungroup() |> dplyr::filter(!is.na(.data$type), grepl(pattern, .data$type)) |> dplyr::select(dplyr::any_of(cols_sel)) diff --git a/R/multiqc.R b/R/multiqc.R index 561b807..7f4d748 100644 --- a/R/multiqc.R +++ b/R/multiqc.R @@ -128,7 +128,7 @@ multiqc_rename_cols <- function(d) { rename_vec <- purrr::set_names(m[["raw"]], m[["clean"]]) d <- dplyr::rename(d, !!!rename_vec) } - return(d) + return(dplyr::distinct(d)) } .multiqc_guess_workflow <- function(p) { diff --git a/R/portal_meta.R b/R/portal_meta.R index 634dbcd..6d5af6d 100644 --- a/R/portal_meta.R +++ b/R/portal_meta.R @@ -462,6 +462,7 @@ meta_main_cols <- function() { #' @param params String containing additional params to pass to the `/workflows` #' endpoint, e.g. `'&type_name=bclconvert'`. #' @param pmeta Path to downloaded portal metadata file, or already parsed metadata tibble. +#' @param account UMCCR portal account (one of "prod", "dev", "stg"). #' #' @return A tibble of the results from the given query. #' @export @@ -471,6 +472,7 @@ meta_main_cols <- function() { #' portal_meta_read(params = "&type_name=rnasum", rows = 4) #' } portal_meta_read <- function(pmeta = NULL, rows = 100, params = "", account = "prod") { + assertthat::assert_that(account %in% c("prod", "dev", "stg")) au_tz <- "Australia/Melbourne" utc_tz <- "UTC" if (!is.null(pmeta)) { diff --git a/inst/extdata/multiqc_column_map.tsv b/inst/extdata/multiqc_column_map.tsv index 0ee0f4e..f70c479 100644 --- a/inst/extdata/multiqc_column_map.tsv +++ b/inst/extdata/multiqc_column_map.tsv @@ -18,6 +18,10 @@ dragen_alignment Mapped reads reads_mapped_dragen dragen_alignment Mapped reads pct reads_mapped_pct_dragen dragen_alignment Mapped reads adjusted for filtered mapping reads_mapped_adjfilt_dragen dragen_alignment Mapped reads adjusted for filtered mapping pct reads_mapped_adjfilt_pct_dragen +dragen_alignment Mapped reads adjusted for excluded mapping reads_mapped_adjexcl_dragen +dragen_alignment Mapped reads adjusted for excluded mapping pct reads_mapped_adjexcl_pct_dragen +dragen_alignment Mapped reads adjusted for filtered and excluded mapping reads_mapped_adjfiltexcl_dragen +dragen_alignment Mapped reads adjusted for filtered and excluded mapping pct reads_mapped_adjfiltexcl_pct_dragen dragen_alignment Mapped reads R1 reads_mapped_r1_dragen dragen_alignment Mapped reads R1 pct reads_mapped_r1_pct_dragen dragen_alignment Mapped reads R2 reads_mapped_r2_dragen @@ -28,6 +32,12 @@ dragen_alignment Unmapped reads reads_unmapped_dragen dragen_alignment Unmapped reads pct reads_unmapped_pct_dragen dragen_alignment Unmapped reads adjusted for filtered mapping reads_unmapped_adjfilt_dragen dragen_alignment Unmapped reads adjusted for filtered mapping pct reads_unmapped_adjfilt_pct_dragen +dragen_alignment Unmapped reads adjusted for excluded mapping reads_unmapped_adjexcl_dragen +dragen_alignment Unmapped reads adjusted for excluded mapping pct reads_unmapped_adjexcl_pct_dragen +dragen_alignment Unmapped reads adjusted for filtered and excluded mapping reads_unmapped_adjfiltexcl_dragen +dragen_alignment Unmapped reads adjusted for filtered and excluded mapping pct reads_unmapped_adjfiltexcl_pct_dragen +dragen_alignment Reads mapping to multiple locations reads_map_multiloc_dragen +dragen_alignment Reads mapping to multiple locations pct reads_map_multiloc_pct_dragen dragen_alignment Adjustment of reads matching non-reference decoys reads_match_nonref_decoys_adj_dragen dragen_alignment Adjustment of reads matching non-reference decoys pct reads_match_nonref_decoys_adj_pct_dragen dragen_alignment Singleton reads (itself mapped; mate unmapped) reads_singleton_dragen @@ -65,10 +75,19 @@ dragen_alignment Mapped bases R1 bases_mapped_r1_dragen dragen_alignment Mapped bases R1 pct bases_mapped_r1_pct_dragen dragen_alignment Mapped bases R2 bases_mapped_r2_dragen dragen_alignment Mapped bases R2 pct bases_mapped_r2_pct_dragen +dragen_alignment Mapped bases bases_mapped_dragen dragen_alignment Soft-clipped bases R1 bases_softclip_r1_dragen dragen_alignment Soft-clipped bases R2 bases_softclip_r2_dragen dragen_alignment Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen dragen_alignment Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen +dragen_alignment Hard-clipped bases R1 bases_hardclip_r1_dragen +dragen_alignment Hard-clipped bases R2 bases_hardclip_r2_dragen +dragen_alignment Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen +dragen_alignment Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen +dragen_alignment Soft-clipped bases bases_softclip_dragen +dragen_alignment Soft-clipped bases pct bases_softclip_pct_dragen +dragen_alignment Hard-clipped bases bases_hardclip_dragen +dragen_alignment Hard-clipped bases pct bases_hardclip_pct_dragen dragen_alignment Mismatched bases R1 bases_mismatched_r1_dragen dragen_alignment Mismatched bases R2 bases_mismatched_r2_dragen dragen_alignment Mismatched bases R1 pct bases_mismatched_r1_pct_dragen @@ -132,6 +151,7 @@ dragen_alignment Aligned bases in genome bases_aligned_in_genome_dragen dragen_alignment Aligned bases in genome pct bases_aligned_in_genome_pct_dragen dragen_alignment Average alignment coverage over genome cov_alignment_avg_over_genome_dragen dragen_alignment Uniformity of coverage (PCT > 0.2*mean) over genome cov_uniformity_over_genome_pct_gt02mean_dragen +dragen_alignment Uniformity of coverage (PCT > 0.4*mean) over genome cov_uniformity_over_genome_pct_gt04mean_dragen dragen_alignment PCT of genome with coverage [100x: inf) cov_genome_pct_100x_inf_dragen dragen_alignment PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen dragen_alignment PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen @@ -147,6 +167,27 @@ dragen_alignment PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_ dragen_alignment PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen dragen_alignment PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen dragen_alignment PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen +dragen_alignment PCT of genome with coverage [1500x: inf) cov_genome_pct_1500x_inf_dragen +dragen_alignment PCT of genome with coverage [1000x: inf) cov_genome_pct_1000x_inf_dragen +dragen_alignment PCT of genome with coverage [ 500x: inf) cov_genome_pct_500x_inf_dragen +dragen_alignment PCT of genome with coverage [ 100x: inf) cov_genome_pct_100x_inf_dragen +dragen_alignment PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen +dragen_alignment PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen +dragen_alignment PCT of genome with coverage [ 15x: inf) cov_genome_pct_15x_inf_dragen +dragen_alignment PCT of genome with coverage [ 10x: inf) cov_genome_pct_10x_inf_dragen +dragen_alignment PCT of genome with coverage [ 3x: inf) cov_genome_pct_3x_inf_dragen +dragen_alignment PCT of genome with coverage [ 1x: inf) cov_genome_pct_1x_inf_dragen +dragen_alignment PCT of genome with coverage [ 0x: inf) cov_genome_pct_0x_inf_dragen +dragen_alignment PCT of genome with coverage [1000x:1500x) cov_genome_pct_1000x_1500x_dragen +dragen_alignment PCT of genome with coverage [ 500x:1000x) cov_genome_pct_500x_1000x_dragen +dragen_alignment PCT of genome with coverage [ 100x: 500x) cov_genome_pct_100x_500x_dragen +dragen_alignment PCT of genome with coverage [ 50x: 100x) cov_genome_pct_50x_100x_dragen +dragen_alignment PCT of genome with coverage [ 20x: 50x) cov_genome_pct_20x_50x_dragen +dragen_alignment PCT of genome with coverage [ 15x: 20x) cov_genome_pct_15x_20x_dragen +dragen_alignment PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dragen +dragen_alignment PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen +dragen_alignment PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen +dragen_alignment PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen dragen_alignment Average chr X coverage over genome cov_avg_x_over_genome_dragen dragen_alignment Average chr Y coverage over genome cov_avg_y_over_genome_dragen dragen_alignment Average mitochondrial coverage over genome cov_avg_mt_over_genome_dragen @@ -176,6 +217,10 @@ dragen_somatic Mapped reads reads_mapped_dragen dragen_somatic Mapped reads pct reads_mapped_pct_dragen dragen_somatic Mapped reads adjusted for filtered mapping reads_mapped_adjfilt_dragen dragen_somatic Mapped reads adjusted for filtered mapping pct reads_mapped_adjfilt_pct_dragen +dragen_somatic Mapped reads adjusted for excluded mapping reads_mapped_adjexcl_dragen +dragen_somatic Mapped reads adjusted for excluded mapping pct reads_mapped_adjexcl_pct_dragen +dragen_somatic Mapped reads adjusted for filtered and excluded mapping reads_mapped_adjfiltexcl_dragen +dragen_somatic Mapped reads adjusted for filtered and excluded mapping pct reads_mapped_adjfiltexcl_pct_dragen dragen_somatic Mapped reads R1 reads_mapped_r1_dragen dragen_somatic Mapped reads R1 pct reads_mapped_r1_pct_dragen dragen_somatic Mapped reads R2 reads_mapped_r2_dragen @@ -186,6 +231,12 @@ dragen_somatic Unmapped reads reads_unmapped_dragen dragen_somatic Unmapped reads pct reads_unmapped_pct_dragen dragen_somatic Unmapped reads adjusted for filtered mapping reads_unmapped_adjfilt_dragen dragen_somatic Unmapped reads adjusted for filtered mapping pct reads_unmapped_adjfilt_pct_dragen +dragen_somatic Unmapped reads adjusted for excluded mapping reads_unmapped_adjexcl_dragen +dragen_somatic Unmapped reads adjusted for excluded mapping pct reads_unmapped_adjexcl_pct_dragen +dragen_somatic Unmapped reads adjusted for filtered and excluded mapping reads_unmapped_adjfiltexcl_dragen +dragen_somatic Unmapped reads adjusted for filtered and excluded mapping pct reads_unmapped_adjfiltexcl_pct_dragen +dragen_somatic Reads mapping to multiple locations reads_map_multiloc_dragen +dragen_somatic Reads mapping to multiple locations pct reads_map_multiloc_pct_dragen dragen_somatic Adjustment of reads matching non-reference decoys reads_match_nonref_decoys_adj_dragen dragen_somatic Adjustment of reads matching non-reference decoys pct reads_match_nonref_decoys_adj_pct_dragen dragen_somatic Singleton reads (itself mapped; mate unmapped) reads_singleton_dragen @@ -227,6 +278,14 @@ dragen_somatic Soft-clipped bases R1 bases_softclip_r1_dragen dragen_somatic Soft-clipped bases R2 bases_softclip_r2_dragen dragen_somatic Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen dragen_somatic Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen +dragen_somatic Hard-clipped bases R1 bases_hardclip_r1_dragen +dragen_somatic Hard-clipped bases R2 bases_hardclip_r2_dragen +dragen_somatic Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen +dragen_somatic Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen +dragen_somatic Soft-clipped bases bases_softclip_dragen +dragen_somatic Soft-clipped bases pct bases_softclip_pct_dragen +dragen_somatic Hard-clipped bases bases_hardclip_dragen +dragen_somatic Hard-clipped bases pct bases_hardclip_pct_dragen dragen_somatic Mismatched bases R1 bases_mismatched_r1_dragen dragen_somatic Mismatched bases R2 bases_mismatched_r2_dragen dragen_somatic Mismatched bases R1 pct bases_mismatched_r1_pct_dragen @@ -290,6 +349,7 @@ dragen_somatic Aligned bases in genome bases_aligned_in_genome_dragen dragen_somatic Aligned bases in genome pct bases_aligned_in_genome_pct_dragen dragen_somatic Average alignment coverage over genome cov_alignment_avg_over_genome_dragen dragen_somatic Uniformity of coverage (PCT > 0.2*mean) over genome cov_uniformity_over_genome_pct_gt02mean_dragen +dragen_somatic Uniformity of coverage (PCT > 0.4*mean) over genome cov_uniformity_over_genome_pct_gt04mean_dragen dragen_somatic PCT of genome with coverage [100x: inf) cov_genome_pct_100x_inf_dragen dragen_somatic PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen dragen_somatic PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen @@ -305,6 +365,27 @@ dragen_somatic PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dr dragen_somatic PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen dragen_somatic PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen dragen_somatic PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen +dragen_somatic PCT of genome with coverage [1500x: inf) cov_genome_pct_1500x_inf_dragen +dragen_somatic PCT of genome with coverage [1000x: inf) cov_genome_pct_1000x_inf_dragen +dragen_somatic PCT of genome with coverage [ 500x: inf) cov_genome_pct_500x_inf_dragen +dragen_somatic PCT of genome with coverage [ 100x: inf) cov_genome_pct_100x_inf_dragen +dragen_somatic PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen +dragen_somatic PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen +dragen_somatic PCT of genome with coverage [ 15x: inf) cov_genome_pct_15x_inf_dragen +dragen_somatic PCT of genome with coverage [ 10x: inf) cov_genome_pct_10x_inf_dragen +dragen_somatic PCT of genome with coverage [ 3x: inf) cov_genome_pct_3x_inf_dragen +dragen_somatic PCT of genome with coverage [ 1x: inf) cov_genome_pct_1x_inf_dragen +dragen_somatic PCT of genome with coverage [ 0x: inf) cov_genome_pct_0x_inf_dragen +dragen_somatic PCT of genome with coverage [1000x:1500x) cov_genome_pct_1000x_1500x_dragen +dragen_somatic PCT of genome with coverage [ 500x:1000x) cov_genome_pct_500x_1000x_dragen +dragen_somatic PCT of genome with coverage [ 100x: 500x) cov_genome_pct_100x_500x_dragen +dragen_somatic PCT of genome with coverage [ 50x: 100x) cov_genome_pct_50x_100x_dragen +dragen_somatic PCT of genome with coverage [ 20x: 50x) cov_genome_pct_20x_50x_dragen +dragen_somatic PCT of genome with coverage [ 15x: 20x) cov_genome_pct_15x_20x_dragen +dragen_somatic PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dragen +dragen_somatic PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen +dragen_somatic PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen +dragen_somatic PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen dragen_somatic Average chr X coverage over genome cov_avg_x_over_genome_dragen dragen_somatic Average chr Y coverage over genome cov_avg_y_over_genome_dragen dragen_somatic Average mitochondrial coverage over genome cov_avg_mt_over_genome_dragen @@ -383,6 +464,10 @@ dragen_transcriptome Mapped reads reads_mapped_dragen dragen_transcriptome Mapped reads pct reads_mapped_pct_dragen dragen_transcriptome Mapped reads adjusted for filtered mapping reads_mapped_adjfilt_dragen dragen_transcriptome Mapped reads adjusted for filtered mapping pct reads_mapped_adjfilt_pct_dragen +dragen_transcriptome Mapped reads adjusted for excluded mapping reads_mapped_adjexcl_dragen +dragen_transcriptome Mapped reads adjusted for excluded mapping pct reads_mapped_adjexcl_pct_dragen +dragen_transcriptome Mapped reads adjusted for filtered and excluded mapping reads_mapped_adjfiltexcl_dragen +dragen_transcriptome Mapped reads adjusted for filtered and excluded mapping pct reads_mapped_adjfiltexcl_pct_dragen dragen_transcriptome Mapped reads R1 reads_mapped_r1_dragen dragen_transcriptome Mapped reads R1 pct reads_mapped_r1_pct_dragen dragen_transcriptome Mapped reads R2 reads_mapped_r2_dragen @@ -393,6 +478,12 @@ dragen_transcriptome Unmapped reads reads_unmapped_dragen dragen_transcriptome Unmapped reads pct reads_unmapped_pct_dragen dragen_transcriptome Unmapped reads adjusted for filtered mapping reads_unmapped_adjfilt_dragen dragen_transcriptome Unmapped reads adjusted for filtered mapping pct reads_unmapped_adjfilt_pct_dragen +dragen_transcriptome Unmapped reads adjusted for excluded mapping reads_unmapped_adjexcl_dragen +dragen_transcriptome Unmapped reads adjusted for excluded mapping pct reads_unmapped_adjexcl_pct_dragen +dragen_transcriptome Unmapped reads adjusted for filtered and excluded mapping reads_unmapped_adjfiltexcl_dragen +dragen_transcriptome Unmapped reads adjusted for filtered and excluded mapping pct reads_unmapped_adjfiltexcl_pct_dragen +dragen_transcriptome Reads mapping to multiple locations reads_map_multiloc_dragen +dragen_transcriptome Reads mapping to multiple locations pct reads_map_multiloc_pct_dragen dragen_transcriptome Adjustment of reads matching non-reference decoys reads_match_nonref_decoys_adj_dragen dragen_transcriptome Adjustment of reads matching non-reference decoys pct reads_match_nonref_decoys_adj_pct_dragen dragen_transcriptome Singleton reads (itself mapped; mate unmapped) reads_singleton_dragen @@ -434,6 +525,14 @@ dragen_transcriptome Soft-clipped bases R1 bases_softclip_r1_dragen dragen_transcriptome Soft-clipped bases R2 bases_softclip_r2_dragen dragen_transcriptome Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen dragen_transcriptome Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen +dragen_transcriptome Hard-clipped bases R1 bases_hardclip_r1_dragen +dragen_transcriptome Hard-clipped bases R2 bases_hardclip_r2_dragen +dragen_transcriptome Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen +dragen_transcriptome Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen +dragen_transcriptome Soft-clipped bases bases_softclip_dragen +dragen_transcriptome Soft-clipped bases pct bases_softclip_pct_dragen +dragen_transcriptome Hard-clipped bases bases_hardclip_dragen +dragen_transcriptome Hard-clipped bases pct bases_hardclip_pct_dragen dragen_transcriptome Mismatched bases R1 bases_mismatched_r1_dragen dragen_transcriptome Mismatched bases R1 pct bases_mismatched_r1_pct_dragen dragen_transcriptome Mismatched bases R2 pct bases_mismatched_r2_pct_dragen @@ -468,6 +567,7 @@ dragen_transcriptome Aligned bases in genome bases_aligned_in_genome_dragen dragen_transcriptome Aligned bases in genome pct bases_aligned_in_genome_pct_dragen dragen_transcriptome Average alignment coverage over genome cov_alignment_avg_over_genome_dragen dragen_transcriptome Uniformity of coverage (PCT > 0.2*mean) over genome cov_uniformity_over_genome_pct_gt02mean_dragen +dragen_transcriptome Uniformity of coverage (PCT > 0.4*mean) over genome cov_uniformity_over_genome_pct_gt04mean_dragen dragen_transcriptome PCT of genome with coverage [100x: inf) cov_genome_pct_100x_inf_dragen dragen_transcriptome PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen dragen_transcriptome PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen @@ -483,6 +583,27 @@ dragen_transcriptome PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_ dragen_transcriptome PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen dragen_transcriptome PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen dragen_transcriptome PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen +dragen_transcriptome PCT of genome with coverage [1500x: inf) cov_genome_pct_1500x_inf_dragen +dragen_transcriptome PCT of genome with coverage [1000x: inf) cov_genome_pct_1000x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 500x: inf) cov_genome_pct_500x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 100x: inf) cov_genome_pct_100x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 15x: inf) cov_genome_pct_15x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 10x: inf) cov_genome_pct_10x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 3x: inf) cov_genome_pct_3x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 1x: inf) cov_genome_pct_1x_inf_dragen +dragen_transcriptome PCT of genome with coverage [ 0x: inf) cov_genome_pct_0x_inf_dragen +dragen_transcriptome PCT of genome with coverage [1000x:1500x) cov_genome_pct_1000x_1500x_dragen +dragen_transcriptome PCT of genome with coverage [ 500x:1000x) cov_genome_pct_500x_1000x_dragen +dragen_transcriptome PCT of genome with coverage [ 100x: 500x) cov_genome_pct_100x_500x_dragen +dragen_transcriptome PCT of genome with coverage [ 50x: 100x) cov_genome_pct_50x_100x_dragen +dragen_transcriptome PCT of genome with coverage [ 20x: 50x) cov_genome_pct_20x_50x_dragen +dragen_transcriptome PCT of genome with coverage [ 15x: 20x) cov_genome_pct_15x_20x_dragen +dragen_transcriptome PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dragen +dragen_transcriptome PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen +dragen_transcriptome PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen +dragen_transcriptome PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen dragen_transcriptome Average chr X coverage over genome cov_avg_x_over_genome_dragen dragen_transcriptome Average chr Y coverage over genome cov_avg_y_over_genome_dragen dragen_transcriptome Average mitochondrial coverage over genome cov_avg_mt_over_genome_dragen @@ -518,6 +639,10 @@ dragen_umccrise Mapped reads reads_mapped_dragen dragen_umccrise Mapped reads pct reads_mapped_pct_dragen dragen_umccrise Mapped reads adjusted for filtered mapping reads_mapped_adjfilt_dragen dragen_umccrise Mapped reads adjusted for filtered mapping pct reads_mapped_adjfilt_pct_dragen +dragen_umccrise Mapped reads adjusted for excluded mapping reads_mapped_adjexcl_dragen +dragen_umccrise Mapped reads adjusted for excluded mapping pct reads_mapped_adjexcl_pct_dragen +dragen_umccrise Mapped reads adjusted for filtered and excluded mapping reads_mapped_adjfiltexcl_dragen +dragen_umccrise Mapped reads adjusted for filtered and excluded mapping pct reads_mapped_adjfiltexcl_pct_dragen dragen_umccrise Mapped reads R1 reads_mapped_r1_dragen dragen_umccrise Mapped reads R1 pct reads_mapped_r1_pct_dragen dragen_umccrise Mapped reads R2 reads_mapped_r2_dragen @@ -528,6 +653,12 @@ dragen_umccrise Unmapped reads reads_unmapped_dragen dragen_umccrise Unmapped reads pct reads_unmapped_pct_dragen dragen_umccrise Unmapped reads adjusted for filtered mapping reads_unmapped_adjfilt_dragen dragen_umccrise Unmapped reads adjusted for filtered mapping pct reads_unmapped_adjfilt_pct_dragen +dragen_umccrise Unmapped reads adjusted for excluded mapping reads_unmapped_adjexcl_dragen +dragen_umccrise Unmapped reads adjusted for excluded mapping pct reads_unmapped_adjexcl_pct_dragen +dragen_umccrise Unmapped reads adjusted for filtered and excluded mapping reads_unmapped_adjfiltexcl_dragen +dragen_umccrise Unmapped reads adjusted for filtered and excluded mapping pct reads_unmapped_adjfiltexcl_pct_dragen +dragen_umccrise Reads mapping to multiple locations reads_map_multiloc_dragen +dragen_umccrise Reads mapping to multiple locations pct reads_map_multiloc_pct_dragen dragen_umccrise Adjustment of reads matching non-reference decoys reads_match_nonref_decoys_adj_dragen dragen_umccrise Adjustment of reads matching non-reference decoys pct reads_match_nonref_decoys_adj_pct_dragen dragen_umccrise Singleton reads (itself mapped; mate unmapped) reads_singleton_dragen @@ -565,10 +696,19 @@ dragen_umccrise Mapped bases R1 bases_mapped_r1_dragen dragen_umccrise Mapped bases R1 pct bases_mapped_r1_pct_dragen dragen_umccrise Mapped bases R2 bases_mapped_r2_dragen dragen_umccrise Mapped bases R2 pct bases_mapped_r2_pct_dragen +dragen_umccrise Mapped bases bases_mapped_dragen dragen_umccrise Soft-clipped bases R1 bases_softclip_r1_dragen dragen_umccrise Soft-clipped bases R2 bases_softclip_r2_dragen dragen_umccrise Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen dragen_umccrise Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen +dragen_umccrise Hard-clipped bases R1 bases_hardclip_r1_dragen +dragen_umccrise Hard-clipped bases R2 bases_hardclip_r2_dragen +dragen_umccrise Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen +dragen_umccrise Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen +dragen_umccrise Soft-clipped bases bases_softclip_dragen +dragen_umccrise Soft-clipped bases pct bases_softclip_pct_dragen +dragen_umccrise Hard-clipped bases bases_hardclip_dragen +dragen_umccrise Hard-clipped bases pct bases_hardclip_pct_dragen dragen_umccrise Mismatched bases R1 bases_mismatched_r1_dragen dragen_umccrise Mismatched bases R2 bases_mismatched_r2_dragen dragen_umccrise Mismatched bases R1 pct bases_mismatched_r1_pct_dragen @@ -632,6 +772,7 @@ dragen_umccrise Aligned bases in genome bases_aligned_in_genome_dragen dragen_umccrise Aligned bases in genome pct bases_aligned_in_genome_pct_dragen dragen_umccrise Average alignment coverage over genome cov_alignment_avg_over_genome_dragen dragen_umccrise Uniformity of coverage (PCT > 0.2*mean) over genome cov_uniformity_over_genome_pct_gt02mean_dragen +dragen_umccrise Uniformity of coverage (PCT > 0.4*mean) over genome cov_uniformity_over_genome_pct_gt04mean_dragen dragen_umccrise PCT of genome with coverage [100x: inf) cov_genome_pct_100x_inf_dragen dragen_umccrise PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen dragen_umccrise PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen @@ -647,6 +788,27 @@ dragen_umccrise PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_d dragen_umccrise PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen dragen_umccrise PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen dragen_umccrise PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen +dragen_umccrise PCT of genome with coverage [1500x: inf) cov_genome_pct_1500x_inf_dragen +dragen_umccrise PCT of genome with coverage [1000x: inf) cov_genome_pct_1000x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 500x: inf) cov_genome_pct_500x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 100x: inf) cov_genome_pct_100x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 15x: inf) cov_genome_pct_15x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 10x: inf) cov_genome_pct_10x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 3x: inf) cov_genome_pct_3x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 1x: inf) cov_genome_pct_1x_inf_dragen +dragen_umccrise PCT of genome with coverage [ 0x: inf) cov_genome_pct_0x_inf_dragen +dragen_umccrise PCT of genome with coverage [1000x:1500x) cov_genome_pct_1000x_1500x_dragen +dragen_umccrise PCT of genome with coverage [ 500x:1000x) cov_genome_pct_500x_1000x_dragen +dragen_umccrise PCT of genome with coverage [ 100x: 500x) cov_genome_pct_100x_500x_dragen +dragen_umccrise PCT of genome with coverage [ 50x: 100x) cov_genome_pct_50x_100x_dragen +dragen_umccrise PCT of genome with coverage [ 20x: 50x) cov_genome_pct_20x_50x_dragen +dragen_umccrise PCT of genome with coverage [ 15x: 20x) cov_genome_pct_15x_20x_dragen +dragen_umccrise PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dragen +dragen_umccrise PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen +dragen_umccrise PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen +dragen_umccrise PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen dragen_umccrise Average chr X coverage over genome cov_avg_x_over_genome_dragen dragen_umccrise Average chr Y coverage over genome cov_avg_y_over_genome_dragen dragen_umccrise Average mitochondrial coverage over genome cov_avg_mt_over_genome_dragen @@ -805,6 +967,7 @@ dragen_umccrise viral_content viral_content_umccrise dragen_umccrise viral_integration_sites viral_integration_sites_umccrise dragen_umccrise germline germline_umccrise dragen_umccrise germline_predispose germline_predispose_umccrise +dragen_umccrise avg_gc_content_percent gc_pct_dragen dragen_ctdna umccr_id umccr_id dragen_ctdna umccr_workflow umccr_workflow dragen_ctdna config_creation_date date_multiqc @@ -892,6 +1055,7 @@ dragen_ctdna Aligned bases in genome bases_aligned_in_genome_dragen dragen_ctdna Aligned bases in genome pct bases_aligned_in_genome_pct_dragen dragen_ctdna Average alignment coverage over genome cov_alignment_avg_over_genome_dragen dragen_ctdna Uniformity of coverage (PCT > 0.2*mean) over genome cov_uniformity_over_genome_pct_gt02mean_dragen +dragen_ctdna Uniformity of coverage (PCT > 0.4*mean) over genome cov_uniformity_over_genome_pct_gt04mean_dragen dragen_ctdna PCT of genome with coverage [100x: inf) cov_genome_pct_100x_inf_dragen dragen_ctdna PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen dragen_ctdna PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen @@ -907,6 +1071,27 @@ dragen_ctdna PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_drag dragen_ctdna PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen dragen_ctdna PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen dragen_ctdna PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen +dragen_ctdna PCT of genome with coverage [1500x: inf) cov_genome_pct_1500x_inf_dragen +dragen_ctdna PCT of genome with coverage [1000x: inf) cov_genome_pct_1000x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 500x: inf) cov_genome_pct_500x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 100x: inf) cov_genome_pct_100x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 50x: inf) cov_genome_pct_50x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 20x: inf) cov_genome_pct_20x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 15x: inf) cov_genome_pct_15x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 10x: inf) cov_genome_pct_10x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 3x: inf) cov_genome_pct_3x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 1x: inf) cov_genome_pct_1x_inf_dragen +dragen_ctdna PCT of genome with coverage [ 0x: inf) cov_genome_pct_0x_inf_dragen +dragen_ctdna PCT of genome with coverage [1000x:1500x) cov_genome_pct_1000x_1500x_dragen +dragen_ctdna PCT of genome with coverage [ 500x:1000x) cov_genome_pct_500x_1000x_dragen +dragen_ctdna PCT of genome with coverage [ 100x: 500x) cov_genome_pct_100x_500x_dragen +dragen_ctdna PCT of genome with coverage [ 50x: 100x) cov_genome_pct_50x_100x_dragen +dragen_ctdna PCT of genome with coverage [ 20x: 50x) cov_genome_pct_20x_50x_dragen +dragen_ctdna PCT of genome with coverage [ 15x: 20x) cov_genome_pct_15x_20x_dragen +dragen_ctdna PCT of genome with coverage [ 10x: 15x) cov_genome_pct_10x_15x_dragen +dragen_ctdna PCT of genome with coverage [ 3x: 10x) cov_genome_pct_3x_10x_dragen +dragen_ctdna PCT of genome with coverage [ 1x: 3x) cov_genome_pct_1x_3x_dragen +dragen_ctdna PCT of genome with coverage [ 0x: 1x) cov_genome_pct_0x_1x_dragen dragen_ctdna Average chr X coverage over genome cov_avg_x_over_genome_dragen dragen_ctdna Average chr Y coverage over genome cov_avg_y_over_genome_dragen dragen_ctdna Average mitochondrial coverage over genome cov_avg_mt_over_genome_dragen @@ -928,6 +1113,14 @@ dragen_ctdna Soft-clipped bases R1 bases_softclip_r1_dragen dragen_ctdna Soft-clipped bases R2 bases_softclip_r2_dragen dragen_ctdna Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen dragen_ctdna Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen +dragen_ctdna Hard-clipped bases R1 bases_hardclip_r1_dragen +dragen_ctdna Hard-clipped bases R2 bases_hardclip_r2_dragen +dragen_ctdna Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen +dragen_ctdna Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen +dragen_ctdna Soft-clipped bases bases_softclip_dragen +dragen_ctdna Soft-clipped bases pct bases_softclip_pct_dragen +dragen_ctdna Hard-clipped bases bases_hardclip_dragen +dragen_ctdna Hard-clipped bases pct bases_hardclip_pct_dragen dragen_ctdna Number of reads reads_umi_dragen dragen_ctdna Number of reads with valid or correctable UMIs reads_validcorrectable_umi_dragen dragen_ctdna Number of reads with valid or correctable UMIs pct reads_validcorrectable_pct_umi_dragen diff --git a/man/gds_files_list_filter_relevant.Rd b/man/gds_files_list_filter_relevant.Rd index e1b0b44..5c5363d 100644 --- a/man/gds_files_list_filter_relevant.Rd +++ b/man/gds_files_list_filter_relevant.Rd @@ -9,7 +9,8 @@ gds_files_list_filter_relevant( token, pattern = NULL, include = NULL, - page_size = 100 + page_size = 100, + regexes = DR_FILE_REGEX ) } \arguments{ @@ -23,6 +24,8 @@ gds_files_list_filter_relevant( \item{page_size}{Page size (def: 100). the GDS directory.} + +\item{regexes}{Tibble with regex and function name.} } \value{ A tibble with type, bname, size, file_id, path, and presigned URL. diff --git a/man/portal_meta_read.Rd b/man/portal_meta_read.Rd index a48c352..786f3e1 100644 --- a/man/portal_meta_read.Rd +++ b/man/portal_meta_read.Rd @@ -4,7 +4,7 @@ \alias{portal_meta_read} \title{Read ICA Workflows Metadata via Portal API} \usage{ -portal_meta_read(pmeta = NULL, rows = 100, params = "") +portal_meta_read(pmeta = NULL, rows = 100, params = "", account = "prod") } \arguments{ \item{pmeta}{Path to downloaded portal metadata file, or already parsed metadata tibble.} @@ -13,6 +13,8 @@ portal_meta_read(pmeta = NULL, rows = 100, params = "") \item{params}{String containing additional params to pass to the \verb{/workflows} endpoint, e.g. \code{'&type_name=bclconvert'}.} + +\item{account}{UMCCR portal account (one of "prod", "dev", "stg").} } \value{ A tibble of the results from the given query. diff --git a/tests/testthat/test-roxytest-testexamples-multiqc.R b/tests/testthat/test-roxytest-testexamples-multiqc.R index 508e22e..225d826 100644 --- a/tests/testthat/test-roxytest-testexamples-multiqc.R +++ b/tests/testthat/test-roxytest-testexamples-multiqc.R @@ -2,7 +2,7 @@ # File R/multiqc.R: @testexamples -test_that("Function multiqc_date_fmt() @ L279", { +test_that("Function multiqc_date_fmt() @ L284", { cdate <- "2023-04-07, 09:09 UTC" (res1 <- multiqc_date_fmt(cdate))