4.3. align_and_plot¶

4.3.1. Inputs¶

align_and_plot.align.reads_unmapped_bam
File — Default: None
???

align_and_plot.align.reference_fasta
File — Default: None
???

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align_and_plot.align.aligner
String — Default: "minimap2"
Short read aligner to use: novoalign, minimap2, or bwa. (Default: novoalign)

align_and_plot.align.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

align_and_plot.align.novocraft_license
File? — Default: None
???

align_and_plot.align.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

align_and_plot.align.skip_mark_dupes
Boolean? — Default: false
???

align_and_plot.aligner_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

align_and_plot.plot_coverage.bin_large_plots
Boolean? — Default: false
???

align_and_plot.plot_coverage.binning_summary_statistic
String? — Default: "max"
???

align_and_plot.plot_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

align_and_plot.plot_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

align_and_plot.plot_coverage.skip_mark_dupes
Boolean? — Default: false
???

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