3.5. assemble_denovo_with_deplete_and_isnv_calling¶
3.5.1. Inputs¶
3.5.1.1. Required inputs¶
assemble_denovo_with_deplete_and_isnv_calling.assemble.trim_clip_db
File — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.raw_reads_unmapped_bam
File — Default: None
unaligned reads in BAM format
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.lastal_db_fasta
File — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.reference_genome_fasta
Array[File]+ — Default: None
???
3.5.1.2. Other inputs¶
Show/Hide
assemble_denovo_with_deplete_and_isnv_calling.assemble.always_succeed
Boolean? — Default: false
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.assembler
String? — Default: "trinity"
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.docker
String? — Default: "quay.io/broadinstitute/viral-assemble"
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.spades_min_contig_len
Int? — Default: 0
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.spades_n_reads
Int? — Default: 10000000
???
assemble_denovo_with_deplete_and_isnv_calling.assemble.trinity_n_reads
Int? — Default: 250000
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.blastDbs
Array[File]? — Default: None
Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.bmtaggerDbs
Array[File]? — Default: None
Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.bwaDbs
Array[File]? — Default: None
Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.clear_tags
Boolean? — Default: false
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.docker
String? — Default: "quay.io/broadinstitute/viral-classify"
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.query_chunk_size
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.deplete_taxa.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.docker
String? — Default: "quay.io/broadinstitute/viral-classify"
???
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.error_on_reads_in_neg_control
Boolean? — Default: false
???
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.neg_control_prefixes_space_separated
String? — Default: "neg water NTC"
???
assemble_denovo_with_deplete_and_isnv_calling.filter_to_taxon.negative_control_reads_threshold
Int? — Default: 0
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.docker
String? — Default: "quay.io/broadinstitute/viral-phylo"
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.maxBias
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.minReadsPerStrand
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.sample_name
String — Default: basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")
???
assemble_denovo_with_deplete_and_isnv_calling.isnvs_per_sample.threads
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.docker
String? — Default: "quay.io/broadinstitute/viral-assemble"
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.novocraft_license
File? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.plot_coverage_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine1_major_cutoff
Float? — Default: 0.5
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine1_min_coverage
Int? — Default: 2
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine1_novoalign_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine2_major_cutoff
Float? — Default: 0.5
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine2_min_coverage
Int? — Default: 3
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.refine2_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100"
???
assemble_denovo_with_deplete_and_isnv_calling.refine_2x_and_plot.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".cleaned")
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.aligner
String? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.docker
String? — Default: "quay.io/broadinstitute/viral-assemble"
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.machine_mem_gb
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.min_length_fraction
Float? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.min_unambig
Float? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.nucmer_max_gap
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.nucmer_min_cluster
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.nucmer_min_match
Int? — Default: None
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.replace_length
Int? — Default: 55
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.sample_name
String — Default: basename(basename(basename(contigs_fasta,".fasta"),".assembly1-trinity"),".assembly1-spades")
???
assemble_denovo_with_deplete_and_isnv_calling.scaffold.scaffold_min_pct_contig_aligned
Float? — Default: None
???
Generated using WDL AID (0.1.1)