diff --git a/inst/extdata/multiqc_column_map.tsv b/inst/extdata/multiqc_column_map.tsv index f70c479..6118473 100644 --- a/inst/extdata/multiqc_column_map.tsv +++ b/inst/extdata/multiqc_column_map.tsv @@ -198,6 +198,7 @@ dragen_alignment Aligned reads reads_aligned_dragen dragen_alignment Aligned reads in genome reads_aligned_in_genome_dragen dragen_alignment Aligned reads in genome pct reads_aligned_in_genome_pct_dragen dragen_alignment Number of duplicate marked and mate reads removed reads_num_dupmarked_mate_reads_removed_dragen +dragen_alignment Number of duplicate marked and mate reads removed pct reads_num_dupmarked_mate_reads_removed_pct_dragen dragen_somatic umccr_id umccr_id dragen_somatic umccr_workflow umccr_workflow dragen_somatic config_creation_date date_multiqc @@ -444,14 +445,19 @@ dragen_somatic Filtered SNPs pct vars_snp_filt_pct_dragen dragen_somatic Filtered indels vars_indel_filt_dragen dragen_somatic Filtered indels pct vars_indel_filt_pct_dragen dragen_somatic Number of duplicate marked and mate reads removed reads_num_dupmarked_mate_reads_removed_dragen +dragen_somatic Number of duplicate marked and mate reads removed pct reads_num_dupmarked_mate_reads_removed_pct_dragen dragen_somatic avg_gc_content_percent gc_pct_dragen dragen_transcriptome umccr_id umccr_id dragen_transcriptome umccr_workflow umccr_workflow dragen_transcriptome config_creation_date date_multiqc dragen_transcriptome Total input reads reads_tot_input_dragen dragen_transcriptome Total input reads pct reads_tot_input_pct_dragen +dragen_transcriptome Total reads in RG reads_tot_rg_dragen +dragen_transcriptome Total reads in RG pct reads_tot_rg_pct_dragen dragen_transcriptome Number of duplicate marked reads reads_num_dupmarked_dragen dragen_transcriptome Number of duplicate marked reads pct reads_num_dupmarked_pct_dragen +dragen_transcriptome Number of duplicate marked and mate reads removed reads_num_dupmarked_mate_reads_removed_dragen +dragen_transcriptome Number of duplicate marked and mate reads removed pct reads_num_dupmarked_mate_reads_removed_pct_dragen dragen_transcriptome Number of unique reads (excl. duplicate marked reads) reads_num_unique_dragen dragen_transcriptome Number of unique reads (excl. duplicate marked reads) pct reads_num_unique_pct_dragen dragen_transcriptome Reads with mate sequenced reads_w_mate_seq_dragen @@ -534,6 +540,7 @@ 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 R2 bases_mismatched_r2_dragen dragen_transcriptome Mismatched bases R1 pct bases_mismatched_r1_pct_dragen dragen_transcriptome Mismatched bases R2 pct bases_mismatched_r2_pct_dragen dragen_transcriptome Mismatched bases R1 (excl. indels) bases_mismatched_r1_noindels_dragen @@ -975,6 +982,7 @@ dragen_ctdna Total input reads reads_tot_input_dragen dragen_ctdna Total input reads pct reads_tot_input_pct_dragen dragen_ctdna Number of duplicate marked reads reads_num_dupmarked_dragen dragen_ctdna Number of duplicate marked reads pct reads_num_dupmarked_pct_dragen +dragen_ctdna Number of duplicate marked and mate reads removed reads_num_dupmarked_mate_reads_removed_dragen dragen_ctdna Number of duplicate marked and mate reads removed pct reads_num_dupmarked_mate_reads_removed_pct_dragen dragen_ctdna Number of unique reads (excl. duplicate marked reads) reads_num_unique_dragen dragen_ctdna Number of unique reads (excl. duplicate marked reads) pct reads_num_unique_pct_dragen @@ -1188,7 +1196,6 @@ dragen_ctdna Reads filtered for minimum read length R1 reads_filt_minreadlenr1_d dragen_ctdna Reads filtered for minimum read length R1 pct reads_filt_minreadlenr1_pct_dragen dragen_ctdna Reads filtered for minimum read length R2 reads_filt_minreadlenr2_dragen dragen_ctdna Reads filtered for minimum read length R2 pct reads_filt_minreadlenr2_pct_dragen -dragen_ctdna Number of duplicate marked and mate reads removed reads_num_dupmarked_mate_reads_removed_dragen dragen_ctdna Total reads in RG reads_tot_rg_dragen dragen_ctdna Total reads in RG pct reads_tot_rg_pct_dragen bcbio_umccrise umccr_id umccr_id