4.44. scaffold_and_refine¶

Scaffold de novo contigs against a set of possible references and subsequently polish with reads.

4.44.1. Inputs¶

scaffold_and_refine.reads_unmapped_bam
File — Default: None
???

scaffold_and_refine.scaffold.contigs_fasta
File — Default: None
???

scaffold_and_refine.scaffold.reference_genome_fasta
Array[File]+ — Default: None
???

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scaffold_and_refine.refine_2x_and_plot.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.10.0"
???

scaffold_and_refine.refine_2x_and_plot.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine_2x_and_plot.novocraft_license
File? — Default: None
???

scaffold_and_refine.refine_2x_and_plot.plot_coverage_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
???

scaffold_and_refine.refine_2x_and_plot.refine1_major_cutoff
Float? — Default: 0.5
???

scaffold_and_refine.refine_2x_and_plot.refine1_min_coverage
Int? — Default: 2
???

scaffold_and_refine.refine_2x_and_plot.refine1_novoalign_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

scaffold_and_refine.refine_2x_and_plot.refine2_major_cutoff
Float? — Default: 0.5
???

scaffold_and_refine.refine_2x_and_plot.refine2_min_coverage
Int? — Default: 3
???

scaffold_and_refine.refine_2x_and_plot.refine2_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100"
???

scaffold_and_refine.refine_2x_and_plot.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".cleaned")
???

scaffold_and_refine.scaffold.aligner
String? — Default: None
???

scaffold_and_refine.scaffold.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.10.0"
???

scaffold_and_refine.scaffold.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.scaffold.min_length_fraction
Float? — Default: None
???

scaffold_and_refine.scaffold.min_unambig
Float? — Default: None
???

scaffold_and_refine.scaffold.nucmer_max_gap
Int? — Default: None
???

scaffold_and_refine.scaffold.nucmer_min_cluster
Int? — Default: None
???

scaffold_and_refine.scaffold.nucmer_min_match
Int? — Default: None
???

scaffold_and_refine.scaffold.replace_length
Int? — Default: 55
???

scaffold_and_refine.scaffold.sample_name
String — Default: basename(basename(contigs_fasta,".fasta"),".assembly1-spades")
???

scaffold_and_refine.scaffold.scaffold_min_pct_contig_aligned
Float? — Default: None
???

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