4.67. scaffold_and_refine

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

4.67.1. Inputs

4.67.1.1. Required 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
???

4.67.1.2. Other common inputs

scaffold_and_refine.refine.sample_name
String — Default: basename(reads_unmapped_bams[0],'.bam')
Base name of output files. The 'SM' field in BAM read group headers are also rewritten to this value. Avoid spaces and other filename-unfriendly characters.

scaffold_and_refine.refine.trim_coords_bed
File? — Default: None
optional primers to trim in reference coordinate space (0-based BED format)

4.67.1.3. Other inputs

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scaffold_and_refine.refine.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.align_to_ref.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

scaffold_and_refine.refine.align_to_ref_options
Map[String,String] — Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 501 -k", "bwa": "-k 12 -B 1", "minimap2": ""}
???

scaffold_and_refine.refine.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.align_to_self.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

scaffold_and_refine.refine.align_to_self_options
Map[String,String] — Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": ""}
???

scaffold_and_refine.refine.aligner
String — Default: "minimap2"
Read aligner software to use. Options: novoalign, bwa, minimap2. Minimap2 can automatically handle Illumina, PacBio, or Oxford Nanopore reads as long as the 'PL' field in the BAM read group header is set properly (novoalign and bwa are Illumina-only).

scaffold_and_refine.refine.alignment_metrics.amplicon_set
String? — Default: None
???

scaffold_and_refine.refine.alignment_metrics.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.alignment_metrics.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine.alignment_metrics.max_amp_len
Int? — Default: 5000
???

scaffold_and_refine.refine.alignment_metrics.max_amplicons
Int? — Default: 500
???

scaffold_and_refine.refine.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???

scaffold_and_refine.refine.call_consensus.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine.call_consensus.mark_duplicates
Boolean — Default: false
???

scaffold_and_refine.refine.isnvs_ref.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???

scaffold_and_refine.refine.isnvs_ref.out_basename
String — Default: basename(aligned_bam,'.bam')
???

scaffold_and_refine.refine.isnvs_self.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???

scaffold_and_refine.refine.isnvs_self.out_basename
String — Default: basename(aligned_bam,'.bam')
???

scaffold_and_refine.refine.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.3.1"
???

scaffold_and_refine.refine.ivar_trim.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

scaffold_and_refine.refine.ivar_trim.min_quality
Int? — Default: 1
Minimum quality threshold for sliding window to pass (Default: 20)

scaffold_and_refine.refine.ivar_trim.primer_offset
Int? — Default: None
???

scaffold_and_refine.refine.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

scaffold_and_refine.refine.major_cutoff
Float — Default: 0.75
If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position. If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.

scaffold_and_refine.refine.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.merge_align_to_ref.reheader_table
File? — Default: None
???

scaffold_and_refine.refine.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.merge_align_to_self.reheader_table
File? — Default: None
???

scaffold_and_refine.refine.min_coverage
Int — Default: 3
Minimum read coverage required to call a position unambiguous.

scaffold_and_refine.refine.novocraft_license
File? — Default: None
The default Novoalign short read aligner is a commercially licensed software that is available in a much slower, single-threaded version for free. If you have a paid license file, provide it here to run in multi-threaded mode. If this is omitted, it will run in single-threaded mode.

scaffold_and_refine.refine.plot_ref_coverage.base_q_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.bin_large_plots
Boolean — Default: false
???

scaffold_and_refine.refine.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

scaffold_and_refine.refine.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.plot_ref_coverage.mapping_q_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.max_coverage_depth
Int? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.plot_height_pixels
Int? — Default: 850
???

scaffold_and_refine.refine.plot_ref_coverage.plot_only_non_duplicates
Boolean — Default: false
???

scaffold_and_refine.refine.plot_ref_coverage.plot_pixels_per_inch
Int? — Default: 100
???

scaffold_and_refine.refine.plot_ref_coverage.plot_width_pixels
Int? — Default: 1100
???

scaffold_and_refine.refine.plot_ref_coverage.plotXLimits
String? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.plotYLimits
String? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.read_length_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???

scaffold_and_refine.refine.plot_self_coverage.base_q_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.bin_large_plots
Boolean — Default: false
???

scaffold_and_refine.refine.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

scaffold_and_refine.refine.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.plot_self_coverage.mapping_q_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.max_coverage_depth
Int? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.plot_height_pixels
Int? — Default: 850
???

scaffold_and_refine.refine.plot_self_coverage.plot_only_non_duplicates
Boolean — Default: false
???

scaffold_and_refine.refine.plot_self_coverage.plot_pixels_per_inch
Int? — Default: 100
???

scaffold_and_refine.refine.plot_self_coverage.plot_width_pixels
Int? — Default: 1100
???

scaffold_and_refine.refine.plot_self_coverage.plotXLimits
String? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.plotYLimits
String? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.read_length_threshold
Int? — Default: None
???

scaffold_and_refine.refine.plot_self_coverage.skip_mark_dupes
Boolean — Default: false
???

scaffold_and_refine.refine.run_discordance.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

scaffold_and_refine.refine.skip_mark_dupes
Boolean — Default: false
skip Picard MarkDuplicates step after alignment. This is recommended to be set to true for PCR amplicon based data. (Default: false)

scaffold_and_refine.scaffold.aligner
String — Default: "muscle"
???

scaffold_and_refine.scaffold.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???

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_contig_len
Int? — Default: None
???

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

4.67.2. Outputs

scaffold_and_refine.aligned_bam
File
???

scaffold_and_refine.aligned_only_reads_bam
File
???

scaffold_and_refine.aligned_only_reads_fastqc
File
???

scaffold_and_refine.assembly_length
Int
???

scaffold_and_refine.assembly_length_unambiguous
Int
???

scaffold_and_refine.assembly_preimpute_length
Int
???

scaffold_and_refine.assembly_preimpute_length_unambiguous
Int
???

scaffold_and_refine.bases_aligned
Float
???

scaffold_and_refine.coverage_plot
File
???

scaffold_and_refine.coverage_tsv
File
???

scaffold_and_refine.final_assembly_fasta
File
???

scaffold_and_refine.intermediate_gapfill_fasta
File
???

scaffold_and_refine.intermediate_scaffold_fasta
File
???

scaffold_and_refine.isnvsFile
File
???

scaffold_and_refine.mean_coverage
Float
???

scaffold_and_refine.num_libraries
Int
???

scaffold_and_refine.num_read_groups
Int
???

scaffold_and_refine.read_pairs_aligned
Int
???

scaffold_and_refine.reads_aligned
Int
???

scaffold_and_refine.refine_viral_assemble_version
String
???

scaffold_and_refine.replicate_concordant_sites
Int
???

scaffold_and_refine.replicate_discordant_indels
Int
???

scaffold_and_refine.replicate_discordant_snps
Int
???

scaffold_and_refine.replicate_discordant_vcf
File
???

scaffold_and_refine.scaffold_fasta
File
???

scaffold_and_refine.scaffold_viral_assemble_version
String
???

scaffold_and_refine.scaffolding_alt_contigs
File
???

scaffold_and_refine.scaffolding_chosen_ref_names
Array[String]
???

scaffold_and_refine.scaffolding_stats
File
???

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