Orchestrates all DRAGEN tools (DragenMap, DragenFqc, DragenCov,
DragenVar, DragenRna, DragenTso) over a shared results directory. A DRAGEN run
exposes a different subset of files depending on the pipeline (germline,
somatic tumor-normal, RNA); tools whose files are absent contribute nothing,
so a single Dragen$run() works across all pipelines.
Super class
nemo::Workflow -> Dragen
Methods
Inherited methods
Examples
indir <- system.file("extdata", package = "tidydragen")
odir <- tempdir()
d <- Dragen$new(indir)
d$run(output_dir = odir, format = "parquet", input_id = "run1")
(lf <- list.files(odir, pattern = "dragen.*parquet", full.names = FALSE))
#> [1] "sampleA_dragenfqc_posbasecontent.parquet"
#> [2] "sampleA_dragenfqc_posbasemeanqual.parquet"
#> [3] "sampleA_dragenfqc_posqual.parquet"
#> [4] "sampleA_dragenfqc_readgc.parquet"
#> [5] "sampleA_dragenfqc_readgcqual.parquet"
#> [6] "sampleA_dragenfqc_readlen.parquet"
#> [7] "sampleA_dragenfqc_readmeanqual.parquet"
#> [8] "sampleA_dragenfqc_seqpos.parquet"
#> [9] "sampleA_dragenmap_fraglenhist.parquet"
#> [10] "sampleA_dragenmap_gcbias.parquet"
#> [11] "sampleA_dragenmap_gcmain.parquet"
#> [12] "sampleA_dragenmap_metrics.parquet"
#> [13] "sampleA_dragenmap_time.parquet"
#> [14] "sampleA_dragenmap_trimmer.parquet"
#> [15] "sampleA_dragenmap_umihist.parquet"
#> [16] "sampleA_dragenmap_umimain.parquet"
#> [17] "sampleA_dragenrna_fusion.parquet"
#> [18] "sampleA_dragenrna_quant.parquet"
#> [19] "sampleA_dragentso_exoncov.parquet"
#> [20] "sampleA_dragentso_fusions.parquet"
#> [21] "sampleA_dragentso_genecov.parquet"
#> [22] "sampleA_dragentso_sarcnv.parquet"
#> [23] "sampleA_dragentso_sarinfo.parquet"
#> [24] "sampleA_dragentso_sarqc.parquet"
#> [25] "sampleA_dragentso_sarsnv.parquet"
#> [26] "sampleA_dragentso_sarsw.parquet"
#> [27] "sampleA_dragentso_sarswds.parquet"
#> [28] "sampleA_dragentso_smallvariants.parquet"
#> [29] "sampleA_dragentso_tmbmsaf.parquet"
#> [30] "sampleA_dragentso_tmbtrace.parquet"
#> [31] "sampleA_dragenvar_cnv.parquet"
#> [32] "sampleA_dragenvar_contamination.parquet"
#> [33] "sampleA_dragenvar_gvcf.parquet"
#> [34] "sampleA_dragenvar_hethom.parquet"
#> [35] "sampleA_dragenvar_hrd.parquet"
#> [36] "sampleA_dragenvar_microsat.parquet"
#> [37] "sampleA_dragenvar_nuctrans.parquet"
#> [38] "sampleA_dragenvar_ploidyratio.parquet"
#> [39] "sampleA_dragenvar_ploidystats.parquet"
#> [40] "sampleA_dragenvar_ploidyvcf.parquet"
#> [41] "sampleA_dragenvar_sv.parquet"
#> [42] "sampleA_dragenvar_tmb.parquet"
#> [43] "sampleA_dragenvar_vc.parquet"
#> [44] "sampleA_exon_dragencov_metricsbins.parquet"
#> [45] "sampleA_exon_dragencov_metricscumu.parquet"
#> [46] "sampleA_exon_dragencov_metricsmain.parquet"
#> [47] "sampleA_target_bed_dragencov_metricsbins.parquet"
#> [48] "sampleA_target_bed_dragencov_metricscumu.parquet"
#> [49] "sampleA_target_bed_dragencov_metricsmain.parquet"
#> [50] "sampleA_umccr_dragencov_readreportbed.parquet"
#> [51] "sampleA_umccr_dragencov_reportbedcumu.parquet"
#> [52] "sampleA_umccr_dragencov_reportbedmain.parquet"
#> [53] "sampleA_wgs_dragencov_contigmean.parquet"
#> [54] "sampleA_wgs_dragencov_finehist.parquet"
#> [55] "sampleA_wgs_dragencov_metricsbins.parquet"
#> [56] "sampleA_wgs_dragencov_metricscumu.parquet"
#> [57] "sampleA_wgs_dragencov_metricsmain.parquet"
#> [58] "sampleA_wgs_normal_dragencov_contigmean.parquet"
#> [59] "sampleA_wgs_tumor_dragencov_contigmean.parquet"
#> [60] "sampleB_dragenvar_cnv.parquet"
#> [61] "sampleB_dragenvar_ploidyratio.parquet"
#> [62] "sampleB_dragenvar_ploidystats.parquet"
#> [63] "sampleB_dragenvar_vc.parquet"