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Merge pull request #137 from /issues/136-sash-multiqc
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MultiQC: add sash support
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@qclayssen
qclayssen authored Oct 4, 2024
2 parents 86730fc + 4ba5e1c commit 73116ac
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Showing 2 changed files with 253 additions and 7 deletions.
26 changes: 19 additions & 7 deletions R/multiqc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
#' x <- "/path/to/multiqc_data.json"
#' mqc <- MultiqcFile$new(x)
#' mqc_parsed <- mqc$read() # or read(mqc)
#' mqc$write(mqc_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")
#' outdir <- "nogit"
#' mqc$write(mqc_parsed, out_dir = outdir, prefix = "SBJ02862_PRJ222112", out_format = "tsv")
#' mqc_plots_parsed <- mqc$read(plot = TRUE, plot_names = "everything")
#' mqc$write(mqc_plots_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "rds")
#' }
Expand Down Expand Up @@ -72,7 +73,7 @@ multiqc_tidy_json <- function(j) {
cdate <- multiqc_date_fmt(cdate)
workflow <- .multiqc_guess_workflow(p)
d <- dracarys::multiqc_parse_gen(p)
if (workflow %in% c("dragen_umccrise", "dragen_somatic")) {
if (workflow %in% c("dragen_umccrise", "dragen_somatic", "dragen_sash")) {
# replace the "NA" strings with NA, else we get a column class error
# due to trying to bind string ('NA') with numeric.
# https://stackoverflow.com/questions/35292757/replace-values-in-list
Expand Down Expand Up @@ -120,7 +121,7 @@ multiqc_rename_cols <- function(d) {
umccr_workflows <- c(
"dragen_alignment", "dragen_somatic",
"dragen_transcriptome", "dragen_umccrise",
"dragen_ctdna",
"dragen_ctdna", "dragen_sash",
"bcbio_umccrise", "bcbio_wgs", "bcbio_wts"
)

Expand Down Expand Up @@ -184,11 +185,22 @@ multiqc_rename_cols <- function(d) {
return(paste0("dragen_", w))
} else if (grepl("^UMCCR MultiQC ctDNA", config_title)) {
return("dragen_ctdna")
} else if (
all(
c(
"PURPLE", "DRAGEN-FastQC",
"Bcftools stats (somatic)", "Bcftools stats (germline)"
) %in% ds
)
) {
return("dragen_sash")
} else {
warning(glue(
"config_title: '{config_title}'.\n",
"Unknown which DRAGEN workflow this MultiQC JSON was generated from",
))
warning(
glue(
"config_title: '{config_title}'.\n",
"Unknown which DRAGEN workflow this MultiQC JSON was generated from"
)
)
return("dragen_unknown")
}
}
Expand Down
234 changes: 234 additions & 0 deletions inst/extdata/multiqc_column_map.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -1763,3 +1763,237 @@ bcbio_wgs predicted_parents_ped_check predicted_parents_ped_check_peddy
bcbio_wgs parent_error_ped_check parent_error_ped_check_peddy
bcbio_wgs sample_duplication_error_ped_check sample_duplication_error_ped_check_peddy
bcbio_wgs rel_difference_ped_check rel_difference_ped_check_peddy
dragen_sash umccr_id umccr_id
dragen_sash umccr_workflow umccr_workflow
dragen_sash config_creation_date date_multiqc
dragen_sash Total input reads reads_tot_input_dragen
dragen_sash Total input reads pct reads_tot_input_pct_dragen
dragen_sash Number of duplicate marked reads reads_num_dupmarked_dragen
dragen_sash Number of duplicate marked reads pct reads_num_dupmarked_pct_dragen
dragen_sash Number of unique reads (excl. duplicate marked reads) pct reads_num_uniq_pct_dragen
dragen_sash Reads with mate sequenced reads_w_mate_seq_dragen
dragen_sash Reads with mate sequenced pct reads_w_mate_seq_pct_dragen
dragen_sash Reads without mate sequenced reads_wo_mate_seq_dragen
dragen_sash Reads without mate sequenced pct reads_wo_mate_seq_pct_dragen
dragen_sash QC-failed reads reads_qcfail_dragen
dragen_sash QC-failed reads pct reads_qcfail_pct_dragen
dragen_sash Mapped reads reads_mapped_dragen
dragen_sash Mapped reads pct reads_mapped_pct_dragen
dragen_sash Mapped reads adjusted for excluded mapping reads_mapped_adjexcl_dragen
dragen_sash Mapped reads adjusted for excluded mapping pct reads_mapped_adjexcl_pct_dragen
dragen_sash Mapped reads adjusted for filtered mapping reads_mapped_adjfilt_dragen
dragen_sash Mapped reads adjusted for filtered mapping pct reads_mapped_adjfilt_pct_dragen
dragen_sash Mapped reads adjusted for filtered and excluded mapping reads_mapped_adjfiltexcl_dragen
dragen_sash Mapped reads adjusted for filtered and excluded mapping pct reads_mapped_adjfiltexcl_pct_dragen
dragen_sash Mapped reads R1 reads_mapped_r1_dragen
dragen_sash Mapped reads R1 pct reads_mapped_r1_pct_dragen
dragen_sash Mapped reads R2 reads_mapped_r2_dragen
dragen_sash Mapped reads R2 pct reads_mapped_r2_pct_dragen
dragen_sash Number of unique & mapped reads (excl. duplicate marked reads) reads_num_uniq_mapped_dragen
dragen_sash Number of unique & mapped reads (excl. duplicate marked reads) pct reads_num_uniq_mapped_pct_dragen
dragen_sash Unmapped reads reads_unmapped_dragen
dragen_sash Unmapped reads pct reads_unmapped_pct_dragen
dragen_sash Unmapped reads adjusted for filtered mapping reads_unmapped_adjfilt_dragen
dragen_sash Unmapped reads adjusted for filtered mapping pct reads_unmapped_adjfilt_pct_dragen
dragen_sash Unmapped reads adjusted for excluded mapping reads_unmapped_adjexcl_dragen
dragen_sash Unmapped reads adjusted for excluded mapping pct reads_unmapped_adjexcl_pct_dragen
dragen_sash Unmapped reads adjusted for filtered and excluded mapping reads_unmapped_adjfiltexcl_dragen
dragen_sash Unmapped reads adjusted for filtered and excluded mapping pct reads_unmapped_adjfiltexcl_pct_dragen
dragen_sash Adjustment of reads matching non-reference decoys reads_match_nonref_decoys_adj_dragen
dragen_sash Adjustment of reads matching non-reference decoys pct reads_match_nonref_decoys_adj_pct_dragen
dragen_sash Singleton reads (itself mapped; mate unmapped) reads_singleton_dragen
dragen_sash Singleton reads (itself mapped; mate unmapped) pct reads_singleton_pct_dragen
dragen_sash Paired reads (itself & mate mapped) reads_paired_dragen
dragen_sash Paired reads (itself & mate mapped) pct reads_paired_pct_dragen
dragen_sash Properly paired reads reads_paired_proper_dragen
dragen_sash Properly paired reads pct reads_paired_proper_pct_dragen
dragen_sash Not properly paired reads (discordant) reads_discordant_dragen
dragen_sash Not properly paired reads (discordant) pct reads_discordant_pct_dragen
dragen_sash Paired reads mapped to different chromosomes reads_paired_mapped_diff_chrom_dragen
dragen_sash Paired reads mapped to different chromosomes pct reads_paired_mapped_diff_chrom_pct_dragen
dragen_sash Paired reads mapped to different chromosomes (MAPQ>=10) reads_paired_mapped_diff_chrom_mapq10_dragen
dragen_sash Paired reads mapped to different chromosomes (MAPQ>=10) pct reads_paired_mapped_diff_chrom_mapq10_pct_dragen
dragen_sash Reads mapping to multiple locations reads_map_multiloc_dragen
dragen_sash Reads mapping to multiple locations pct reads_map_multiloc_pct_dragen
dragen_sash Reads with MAPQ [40:inf) reads_mapq_40_inf_dragen
dragen_sash Reads with MAPQ [40:inf) pct reads_mapq_40_inf_pct_dragen
dragen_sash Reads with MAPQ [30:40) reads_mapq_30_40_dragen
dragen_sash Reads with MAPQ [30:40) pct reads_mapq_30_40_pct_dragen
dragen_sash Reads with MAPQ [20:30) reads_mapq_20_30_dragen
dragen_sash Reads with MAPQ [20:30) pct reads_mapq_20_30_pct_dragen
dragen_sash Reads with MAPQ [10:20) reads_mapq_10_20_dragen
dragen_sash Reads with MAPQ [10:20) pct reads_mapq_10_20_pct_dragen
dragen_sash Reads with MAPQ [ 0:10) reads_mapq_0_10_dragen
dragen_sash Reads with MAPQ [ 0:10) pct reads_mapq_0_10_pct_dragen
dragen_sash Reads with MAPQ NA (Unmapped reads) reads_mapq_na_unmapped_dragen
dragen_sash Reads with MAPQ NA (Unmapped reads) pct reads_mapq_na_unmapped_pct_dragen
dragen_sash Reads with indel R1 reads_indel_r1_dragen
dragen_sash Reads with indel R1 pct reads_indel_r1_pct_dragen
dragen_sash Reads with indel R2 reads_indel_r2_dragen
dragen_sash Reads with indel R2 pct reads_indel_r2_pct_dragen
dragen_sash Total bases bases_tot_dragen
dragen_sash Total bases R1 bases_tot_r1_dragen
dragen_sash Total bases R2 bases_tot_r2_dragen
dragen_sash Mapped bases bases_mapped_dragen
dragen_sash Mapped bases R1 bases_mapped_r1_dragen
dragen_sash Mapped bases R2 bases_mapped_r2_dragen
dragen_sash Soft-clipped bases bases_softclip_dragen
dragen_sash Soft-clipped bases pct bases_softclip_pct_dragen
dragen_sash Soft-clipped bases R1 bases_softclip_r1_dragen
dragen_sash Soft-clipped bases R1 pct bases_softclip_r1_pct_dragen
dragen_sash Soft-clipped bases R2 pct bases_softclip_r2_pct_dragen
dragen_sash Hard-clipped bases bases_hardclip_dragen
dragen_sash Hard-clipped bases pct bases_hardclip_pct_dragen
dragen_sash Hard-clipped bases R1 bases_hardclip_r1_dragen
dragen_sash Hard-clipped bases R1 pct bases_hardclip_r1_pct_dragen
dragen_sash Hard-clipped bases R2 bases_hardclip_r2_dragen
dragen_sash Hard-clipped bases R2 pct bases_hardclip_r2_pct_dragen
dragen_sash Mismatched bases R1 bases_mismatched_r1_dragen
dragen_sash Mismatched bases R1 pct bases_mismatched_r1_pct_dragen
dragen_sash Mismatched bases R2 pct bases_mismatched_r2_pct_dragen
dragen_sash Mismatched bases R1 (excl. indels) bases_mismatched_r1_noindels_dragen
dragen_sash Mismatched bases R1 (excl. indels) pct bases_mismatched_r1_noindels_pct_dragen
dragen_sash Mismatched bases R2 (excl. indels) pct bases_mismatched_r2_noindels_pct_dragen
dragen_sash Q30 bases bases_q30_dragen
dragen_sash Q30 bases pct bases_q30_pct_dragen
dragen_sash Q30 bases R1 bases_q30_r1_dragen
dragen_sash Q30 bases R1 pct bases_q30_r1_pct_dragen
dragen_sash Q30 bases R2 bases_q30_r2_dragen
dragen_sash Q30 bases R2 pct bases_q30_r2_pct_dragen
dragen_sash Q30 bases (excl. dups & clipped bases) bases_q30_nodups_noclipped_dragen
dragen_sash Total alignments alignments_tot_dragen
dragen_sash Secondary alignments alignments_secondary_dragen
dragen_sash Supplementary (chimeric) alignments alignments_chimeric_dragen
dragen_sash Estimated read length read_len_dragen
dragen_sash Bases in reference genome bases_in_ref_genome_dragen
dragen_sash Insert length: mean insert_len_mean_dragen
dragen_sash Insert length: median insert_len_median_dragen
dragen_sash Insert length: standard deviation insert_len_std_dev_dragen
dragen_sash DRAGEN mapping rate [mil. reads/second] mapping_rate_dragen_milreads_per_sec_dragen
dragen_sash Secondary alignments pct alignments_secondary_pct_dragen
dragen_sash Q30 bases (excl. dups & clipped bases) pct bases_q30_nodups_noclipped_pct_dragen
dragen_sash Mapped bases R1 pct bases_mapped_r1_pct_dragen
dragen_sash Mapped bases R2 pct bases_mapped_r2_pct_dragen
dragen_sash Total var_tot_dragen
dragen_sash Total pct var_tot_pct_dragen
dragen_sash Biallelic var_biallelic_dragen
dragen_sash Biallelic pct var_biallelic_pct_dragen
dragen_sash Multiallelic var_multiallelic_dragen
dragen_sash Multiallelic pct var_multiallelic_pct_dragen
dragen_sash SNPs var_snp_dragen
dragen_sash SNPs pct var_snp_pct_dragen
dragen_sash Insertions (Hom) var_ins_hom_dragen
dragen_sash Insertions (Hom) pct var_ins_hom_pct_dragen
dragen_sash Insertions (Het) var_ins_het_dragen
dragen_sash Insertions (Het) pct var_ins_het_pct_dragen
dragen_sash Deletions (Hom) var_del_hom_dragen
dragen_sash Deletions (Hom) pct var_del_hom_pct_dragen
dragen_sash Deletions (Het) var_del_het_dragen
dragen_sash Deletions (Het) pct var_del_het_pct_dragen
dragen_sash Indels (Het) var_indel_het_dragen
dragen_sash Indels (Het) pct var_indel_het_pct_dragen
dragen_sash Chr X number of SNPs over genome var_snp_x_over_genome_dragen
dragen_sash Chr Y number of SNPs over genome var_snp_y_over_genome_dragen
dragen_sash (Chr X SNPs)/(chr Y SNPs) ratio over genome var_x_over_y_snp_ratio_over_genome_dragen
dragen_sash SNP Transitions var_snp_transitions_dragen
dragen_sash SNP Transversions var_snp_transversions_dragen
dragen_sash Ti/Tv ratio var_ti_tv_ratio_dragen
dragen_sash Heterozygous var_heterozygous_dragen
dragen_sash Homozygous var_homozygous_dragen
dragen_sash Het/Hom ratio var_het_hom_ratio_dragen
dragen_sash In dbSNP var_in_dbsnp_dragen
dragen_sash In dbSNP pct var_in_dbsnp_pct_dragen
dragen_sash Not in dbSNP var_nin_dbsnp_dragen
dragen_sash Not in dbSNP pct var_nin_dbsnp_pct_dragen
dragen_sash Percent Callability callability_pct_dragen
dragen_sash Percent Autosome Callability callability_auto_pct_dragen
dragen_sash Insertions var_ins_tot_dragen
dragen_sash Deletions var_del_tot_dragen
dragen_sash Indels var_indel_tot_dragen
dragen_sash Insertions pct var_ins_tot_pct_dragen
dragen_sash Deletions pct var_del_tot_pct_dragen
dragen_sash Indels pct var_indel_tot_pct_dragen
dragen_sash Number of samples sample_num_dragen
dragen_sash Reads Processed reads_processed_dragen
dragen_sash Child Sample sample_child_dragen
dragen_sash Filtered vars vars_tot_filt_dragen
dragen_sash Filtered SNPs vars_snp_filt_dragen
dragen_sash Filtered indels vars_indel_filt_dragen
dragen_sash Filtered vars pct vars_tot_filt_pct_dragen
dragen_sash Filtered SNPs pct vars_snp_filt_pct_dragen
dragen_sash Autosomal median coverage cov_auto_median_dragen
dragen_sash X median coverage cov_x_median_dragen
dragen_sash Y median coverage cov_y_median_dragen
dragen_sash 1 median / Autosomal median cov_1_div_auto_medians_dragen
dragen_sash 2 median / Autosomal median cov_2_div_auto_medians_dragen
dragen_sash 3 median / Autosomal median cov_3_div_auto_medians_dragen
dragen_sash 4 median / Autosomal median cov_4_div_auto_medians_dragen
dragen_sash 5 median / Autosomal median cov_5_div_auto_medians_dragen
dragen_sash 6 median / Autosomal median cov_6_div_auto_medians_dragen
dragen_sash 7 median / Autosomal median cov_7_div_auto_medians_dragen
dragen_sash 8 median / Autosomal median cov_8_div_auto_medians_dragen
dragen_sash 9 median / Autosomal median cov_9_div_auto_medians_dragen
dragen_sash 10 median / Autosomal median cov_10_div_auto_median_dragen
dragen_sash 11 median / Autosomal median cov_11_div_auto_median_dragen
dragen_sash 12 median / Autosomal median cov_12_div_auto_median_dragen
dragen_sash 13 median / Autosomal median cov_13_div_auto_median_dragen
dragen_sash 14 median / Autosomal median cov_14_div_auto_median_dragen
dragen_sash 15 median / Autosomal median cov_15_div_auto_median_dragen
dragen_sash 16 median / Autosomal median cov_16_div_auto_median_dragen
dragen_sash 17 median / Autosomal median cov_17_div_auto_median_dragen
dragen_sash 18 median / Autosomal median cov_18_div_auto_median_dragen
dragen_sash 19 median / Autosomal median cov_19_div_auto_median_dragen
dragen_sash 20 median / Autosomal median cov_20_div_auto_median_dragen
dragen_sash 21 median / Autosomal median cov_21_div_auto_median_dragen
dragen_sash 22 median / Autosomal median cov_22_div_auto_median_dragen
dragen_sash X median / Autosomal median cov_x_div_auto_median_dragen
dragen_sash Y median / Autosomal median cov_y_div_auto_median_dragen
dragen_sash Ploidy estimation ploidy_est_dragen
dragen_sash wgs average alignment coverage over genome cov_avg_genome_dragen
dragen_sash QCStatus qc_status_purple
dragen_sash Method method_purple
dragen_sash CopyNumberSegments cn_segs_purple
dragen_sash UnsupportedCopyNumberSegments unsupported_cn_segs_purple
dragen_sash Purity purity_purple1
dragen_sash AmberGender gender_amber
dragen_sash CobaltGender gender_cobalt
dragen_sash DeletedGenes deleted_genes_purple
dragen_sash Contamination contamination_purple
dragen_sash GermlineAberrations germline_aberrations_purple
dragen_sash AmberMeanDepth avg_depth_amber
dragen_sash LohPercent loh_pct_purple
dragen_sash purity purity_purple2
dragen_sash normFactor normfactor_purple
dragen_sash score score_purple
dragen_sash diploidProportion diploid_prop_purple
dragen_sash ploidy ploidy_purple1
dragen_sash gender gender_purple
dragen_sash status status_purple
dragen_sash polyclonalProportion polyclonal_prop_purple
dragen_sash minPurity min_purity_purple
dragen_sash maxPurity max_purity_purple
dragen_sash minPloidy min_ploidy_purple
dragen_sash maxPloidy max_ploidy_purple
dragen_sash minDiploidProportion min_diploid_prop_purple
dragen_sash maxDiploidProportion max_diploid_prop_purple
dragen_sash somaticPenalty somatic_penalty_purple
dragen_sash wholeGenomeDuplication whole_genome_dup_purple
dragen_sash msIndelsPerMb ms_indels_permb_purple
dragen_sash msStatus ms_status_purple
dragen_sash tml tml_purple
dragen_sash tmlStatus tml_status_purple
dragen_sash tmbPerMb tmb_permb_purple
dragen_sash tmbStatus tmb_status_purple
dragen_sash svTumorMutationalBurden tmb_sv_purple
dragen_sash runMode run_mode_purple
dragen_sash targeted targeted_purple
dragen_sash filt_indels var_filt_indels_pct_sash
dragen_sash filt_others var_filt_other_pct_sash
dragen_sash filt_snps var_filt_snps_pct_sash
dragen_sash filt_vars var_filt_vars_pct_sash
dragen_sash indels var_indels_sash
dragen_sash others var_others_sash
dragen_sash snps var_snps_sash
dragen_sash avg_gc_content_percent gc_pct_dragen
dragen_sash germline var_germline_sash
dragen_sash germline_predispose var_germline_predispose_sash

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