4.3. align_and_plot

Align reads to reference and produce coverage plots and statistics.

4.3.1. Inputs

4.3.1.1. Required inputs

align_and_plot.align.reads_unmapped_bam
File — Default: None
Unaligned reads in BAM format.

align_and_plot.align.reference_fasta
File — Default: None
Reference genome, in FASTA format, pre-indexed by Novoindex

4.3.1.2. Advanced inputs

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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.skip_mark_dupes
Boolean? — Default: false
If specific, duplicate reads will not be marked in the resulting output file.

4.3.1.3. Other inputs

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align_and_plot.align.aligner_options
String? — Default: None
???

align_and_plot.align.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

align_and_plot.align.machine_mem_gb
Int? — Default: None
???

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.plot_coverage.base_q_threshold
Int? — Default: None
???

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:2.1.33"
???

align_and_plot.plot_coverage.mapping_q_threshold
Int? — Default: None
???

align_and_plot.plot_coverage.max_coverage_depth
Int? — Default: None
???

align_and_plot.plot_coverage.plot_height_pixels
Int? — Default: 850
???

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

align_and_plot.plot_coverage.plot_pixels_per_inch
Int? — Default: 100
???

align_and_plot.plot_coverage.plot_width_pixels
Int? — Default: 1100
???

align_and_plot.plot_coverage.plotXLimits
String? — Default: None
???

align_and_plot.plot_coverage.plotYLimits
String? — Default: None
???

align_and_plot.plot_coverage.read_length_threshold
Int? — Default: None
???

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

4.3.2. Outputs

align_and_plot.align_viral_core_version
String
???

align_and_plot.aligned_bam
File
???

align_and_plot.aligned_bam_flagstat
File
???

align_and_plot.aligned_bam_idx
File
???

align_and_plot.aligned_only_reads_bam
File
???

align_and_plot.aligned_only_reads_bam_idx
File
???

align_and_plot.aligned_only_reads_fastqc
File
???

align_and_plot.aligned_only_reads_fastqc_zip
File
???

align_and_plot.bases_aligned
Float
???

align_and_plot.coverage_plot
File
???

align_and_plot.coverage_tsv
File
???

align_and_plot.mean_coverage
Float
???

align_and_plot.plot_viral_core_version
String
???

align_and_plot.read_pairs_aligned
Int
???

align_and_plot.reads_aligned
Int
???

align_and_plot.reads_provided
Int
???

align_and_plot.reference_length
Int
???

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