scaffold_and_refine

WORKFLOW scaffold_and_refine

File Path	`pipes/WDL/workflows/scaffold_and_refine.wdl`
WDL Version	1.0
Type	workflow

Imports

Namespace	Path
`assembly`	`../tasks/tasks_assembly.wdl`
`assemble_refbased`	`assemble_refbased.wdl`

Workflow: scaffold_and_refine

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

Author: Broad Viral Genomics

viral-ngs@broadinstitute.org

Inputs

Name	Type	Description	Default
`reads_unmapped_bam`	`File`	-	-
`contigs_fasta`	`File`	-	-
`reference_genome_fasta`	`Array[File]+`	-	-
`min_length_fraction`	`Float?`	-	-
`min_unambig`	`Float?`	-	-
`skani_m`	`Int?`	-	-
`skani_s`	`Int?`	-	-
`skani_c`	`Int?`	-	-
`nucmer_max_gap`	`Int?`	-	-
`nucmer_min_match`	`Int?`	-	-
`nucmer_min_cluster`	`Int?`	-	-
`scaffold_min_contig_len`	`Int?`	-	-
`scaffold_min_pct_contig_aligned`	`Float?`	-	-
`machine_mem_gb`	`Int?`	-	-
`sample_original_name`	`String?`	-	-
`novocraft_license`	`File?`	-	-
`trim_coords_bed`	`File?`	-	-
`machine_mem_gb`	`Int?`	-	-
`min_keep_length`	`Int?`	-	-
`sliding_window`	`Int?`	-	-
`primer_offset`	`Int?`	-	-
`machine_mem_gb`	`Int?`	-	-
`reheader_table`	`File?`	-	-
`amplicon_set`	`String?`	-	-
`max_coverage_depth`	`Int?`	-	-
`base_q_threshold`	`Int?`	-	-
`mapping_q_threshold`	`Int?`	-	-
`read_length_threshold`	`Int?`	-	-
`plotXLimits`	`String?`	-	-
`plotYLimits`	`String?`	-	-
`machine_mem_gb`	`Int?`	-	-
`reheader_table`	`File?`	-	-
`max_coverage_depth`	`Int?`	-	-
`base_q_threshold`	`Int?`	-	-
`mapping_q_threshold`	`Int?`	-	-
`read_length_threshold`	`Int?`	-	-
`plotXLimits`	`String?`	-	-
`plotYLimits`	`String?`	-	-
56 optional inputs with default values
`aligner`	`String`	-	"muscle"
`replace_length`	`Int`	-	55
`allow_incomplete_output`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-assemble:2.5.1.0"
`sample_name`	`String`	-	basename(basename(contigs_fasta,".fasta"),".assembly1-spades")
`sample_name`	`String`	-	basename(reads_unmapped_bams[0],'.bam')
`aligner`	`String`	-	"minimap2"
`min_coverage`	`Int`	-	3
`major_cutoff`	`Float`	-	0.75
`skip_mark_dupes`	`Boolean`	-	false
`align_to_ref_options`	`Map[String,String]`	-	{"novoalign": "-r Random -l 40 -g 40 -x 20 -t 501 -k", "bwa": "-k 12 -B 1", "minimap2": ""}
`align_to_self_options`	`Map[String,String]`	-	{"novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": ""}
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`sample_name`	`String`	-	basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
`min_quality`	`Int?`	-	1
`docker`	`String`	-	"andersenlabapps/ivar:1.3.1"
`bam_basename`	`String`	-	basename(aligned_bam,".bam")
`disk_size`	`Int`	-	375
`run_fastqc`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`disk_size`	`Int`	-	750
`machine_mem_gb`	`Int`	-	4
`out_basename`	`String`	-	basename(aligned_bam,'.bam')
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"
`max_amp_len`	`Int`	-	5000
`max_amplicons`	`Int`	-	500
`machine_mem_gb`	`Int`	-	32
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`skip_mark_dupes`	`Boolean`	-	false
`plot_only_non_duplicates`	`Boolean`	-	false
`bin_large_plots`	`Boolean`	-	false
`binning_summary_statistic`	`String?`	-	"max"
`plot_width_pixels`	`Int?`	-	1100
`plot_height_pixels`	`Int?`	-	850
`plot_pixels_per_inch`	`Int?`	-	100
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`mark_duplicates`	`Boolean`	-	false
`machine_mem_gb`	`Int`	-	15
`docker`	`String`	-	"quay.io/broadinstitute/viral-assemble:2.5.1.0"
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`sample_name`	`String`	-	basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
`run_fastqc`	`Boolean`	-	false
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"
`disk_size`	`Int`	-	750
`machine_mem_gb`	`Int`	-	4
`out_basename`	`String`	-	basename(aligned_bam,'.bam')
`docker`	`String`	-	"quay.io/broadinstitute/viral-phylo:2.5.1.0"
`skip_mark_dupes`	`Boolean`	-	false
`plot_only_non_duplicates`	`Boolean`	-	false
`bin_large_plots`	`Boolean`	-	false
`binning_summary_statistic`	`String?`	-	"max"
`plot_width_pixels`	`Int?`	-	1100
`plot_height_pixels`	`Int?`	-	850
`plot_pixels_per_inch`	`Int?`	-	100
`docker`	`String`	-	"quay.io/broadinstitute/viral-core:2.5.1"

Outputs

Name	Type	Expression
`final_assembly_fasta`	`File`	`refine.assembly_fasta`
`aligned_only_reads_bam`	`File`	`refine.align_to_self_merged_aligned_only_bam`
`coverage_plot`	`File`	`refine.align_to_self_merged_coverage_plot`
`assembly_length`	`Int`	`refine.assembly_length`
`assembly_length_unambiguous`	`Int`	`refine.assembly_length_unambiguous`
`reads_aligned`	`Int`	`refine.align_to_self_merged_reads_aligned`
`mean_coverage`	`Float`	`refine.align_to_self_merged_mean_coverage`
`scaffold_fasta`	`File`	`scaffold.scaffold_fasta`
`intermediate_scaffold_fasta`	`File`	`scaffold.intermediate_scaffold_fasta`
`intermediate_gapfill_fasta`	`File`	`scaffold.intermediate_gapfill_fasta`
`assembly_preimpute_length`	`Int`	`scaffold.assembly_preimpute_length`
`assembly_preimpute_length_unambiguous`	`Int`	`scaffold.assembly_preimpute_length_unambiguous`
`scaffolding_chosen_ref_names`	`Array[String]`	`scaffold.scaffolding_chosen_ref_names`
`scaffolding_stats`	`File`	`scaffold.scaffolding_stats`
`scaffolding_alt_contigs`	`File`	`scaffold.scaffolding_alt_contigs`
`replicate_concordant_sites`	`Int`	`refine.replicate_concordant_sites`
`replicate_discordant_snps`	`Int`	`refine.replicate_discordant_snps`
`replicate_discordant_indels`	`Int`	`refine.replicate_discordant_indels`
`num_read_groups`	`Int`	`refine.num_read_groups`
`num_libraries`	`Int`	`refine.num_libraries`
`replicate_discordant_vcf`	`File`	`refine.replicate_discordant_vcf`
`isnvsFile`	`File`	`refine.align_to_self_isnvs_vcf`
`aligned_bam`	`File`	`refine.align_to_self_merged_aligned_only_bam`
`aligned_only_reads_fastqc`	`File`	`refine.align_to_ref_fastqc`
`coverage_tsv`	`File`	`refine.align_to_self_merged_coverage_tsv`
`read_pairs_aligned`	`Int`	`refine.align_to_self_merged_read_pairs_aligned`
`bases_aligned`	`Float`	`refine.align_to_self_merged_bases_aligned`
`assembly_method`	`String`	`"viral-ngs/scaffold_and_refine"`
`scaffold_viral_assemble_version`	`String`	`scaffold.viralngs_version`
`refine_viral_assemble_version`	`String`	`refine.viral_assemble_version`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `scaffold` ↗

Input Mappings (1)

Input	Value
`reads_bam`	`reads_unmapped_bam`

CALL WORKFLOW `refine` ↗ → assemble_refbased

Input Mappings (2)

Input	Value
`reads_unmapped_bams`	`[reads_unmapped_bam]`
`reference_fasta`	`scaffold.scaffold_fasta`

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

scaffold

← Back to Index

flowchart TD
    Start([scaffold_and_refine])
    N1["scaffold"]
    N2[/"refine
assemble_refbased"/]
    N1 --> N2
    Start --> N1
    N2 --> End([End])
    classDef taskNode fill:#a371f7,stroke:#8b5cf6,stroke-width:2px,color:#fff
    classDef workflowNode fill:#58a6ff,stroke:#1f6feb,stroke-width:2px,color:#fff

version 1.0

import "../tasks/tasks_assembly.wdl" as assembly
import "assemble_refbased.wdl" as assemble_refbased

workflow scaffold_and_refine {
    meta {
        description: "Scaffold de novo contigs against a set of possible references and subsequently polish with reads."
        author: "Broad Viral Genomics"
        email:  "viral-ngs@broadinstitute.org"
        allowNestedInputs: true
    }

    input {
        File reads_unmapped_bam
    }

    call assembly.scaffold {
        input:
            reads_bam = reads_unmapped_bam
    }

    call assemble_refbased.assemble_refbased as refine {
        input:
            reads_unmapped_bams = [reads_unmapped_bam],
            reference_fasta     = scaffold.scaffold_fasta
    }

  output {
    File   final_assembly_fasta                  = refine.assembly_fasta
    File   aligned_only_reads_bam                = refine.align_to_self_merged_aligned_only_bam
    File   coverage_plot                         = refine.align_to_self_merged_coverage_plot
    Int    assembly_length                       = refine.assembly_length
    Int    assembly_length_unambiguous           = refine.assembly_length_unambiguous
    Int    reads_aligned                         = refine.align_to_self_merged_reads_aligned
    Float  mean_coverage                         = refine.align_to_self_merged_mean_coverage
    
    File   scaffold_fasta                        = scaffold.scaffold_fasta
    File   intermediate_scaffold_fasta           = scaffold.intermediate_scaffold_fasta
    File   intermediate_gapfill_fasta            = scaffold.intermediate_gapfill_fasta
    Int    assembly_preimpute_length             = scaffold.assembly_preimpute_length
    Int    assembly_preimpute_length_unambiguous = scaffold.assembly_preimpute_length_unambiguous
    Array[String]  scaffolding_chosen_ref_names  = scaffold.scaffolding_chosen_ref_names
    File   scaffolding_stats                     = scaffold.scaffolding_stats
    File   scaffolding_alt_contigs               = scaffold.scaffolding_alt_contigs

    Int    replicate_concordant_sites            = refine.replicate_concordant_sites
    Int    replicate_discordant_snps             = refine.replicate_discordant_snps
    Int    replicate_discordant_indels           = refine.replicate_discordant_indels
    Int    num_read_groups                       = refine.num_read_groups
    Int    num_libraries                         = refine.num_libraries
    File   replicate_discordant_vcf              = refine.replicate_discordant_vcf

    File   isnvsFile                             = refine.align_to_self_isnvs_vcf
    
    File   aligned_bam                           = refine.align_to_self_merged_aligned_only_bam
    File   aligned_only_reads_fastqc             = refine.align_to_ref_fastqc
    File   coverage_tsv                          = refine.align_to_self_merged_coverage_tsv
    Int    read_pairs_aligned                    = refine.align_to_self_merged_read_pairs_aligned
    Float  bases_aligned                         = refine.align_to_self_merged_bases_aligned
    
    String assembly_method = "viral-ngs/scaffold_and_refine"
    String scaffold_viral_assemble_version       = scaffold.viralngs_version
    String refine_viral_assemble_version         = refine.viral_assemble_version
  }
}

version 1.0 import "../tasks/tasks_assembly.wdl" as assembly import "assemble_refbased.wdl" as assemble_refbased workflow scaffold_and_refine { meta { description: "Scaffold de novo contigs against a set of possible references and subsequently polish with reads." author: "Broad Viral Genomics" email: "viral-ngs@broadinstitute.org" allowNestedInputs: true } input { File reads_unmapped_bam } call assembly.scaffold { input: reads_bam = reads_unmapped_bam } call assemble_refbased.assemble_refbased as refine { input: reads_unmapped_bams = [reads_unmapped_bam], reference_fasta = scaffold.scaffold_fasta } output { File final_assembly_fasta = refine.assembly_fasta File aligned_only_reads_bam = refine.align_to_self_merged_aligned_only_bam File coverage_plot = refine.align_to_self_merged_coverage_plot Int assembly_length = refine.assembly_length Int assembly_length_unambiguous = refine.assembly_length_unambiguous Int reads_aligned = refine.align_to_self_merged_reads_aligned Float mean_coverage = refine.align_to_self_merged_mean_coverage File scaffold_fasta = scaffold.scaffold_fasta File intermediate_scaffold_fasta = scaffold.intermediate_scaffold_fasta File intermediate_gapfill_fasta = scaffold.intermediate_gapfill_fasta Int assembly_preimpute_length = scaffold.assembly_preimpute_length Int assembly_preimpute_length_unambiguous = scaffold.assembly_preimpute_length_unambiguous Array[String] scaffolding_chosen_ref_names = scaffold.scaffolding_chosen_ref_names File scaffolding_stats = scaffold.scaffolding_stats File scaffolding_alt_contigs = scaffold.scaffolding_alt_contigs Int replicate_concordant_sites = refine.replicate_concordant_sites Int replicate_discordant_snps = refine.replicate_discordant_snps Int replicate_discordant_indels = refine.replicate_discordant_indels Int num_read_groups = refine.num_read_groups Int num_libraries = refine.num_libraries File replicate_discordant_vcf = refine.replicate_discordant_vcf File isnvsFile = refine.align_to_self_isnvs_vcf File aligned_bam = refine.align_to_self_merged_aligned_only_bam File aligned_only_reads_fastqc = refine.align_to_ref_fastqc File coverage_tsv = refine.align_to_self_merged_coverage_tsv Int read_pairs_aligned = refine.align_to_self_merged_read_pairs_aligned Float bases_aligned = refine.align_to_self_merged_bases_aligned String assembly_method = "viral-ngs/scaffold_and_refine" String scaffold_viral_assemble_version = scaffold.viralngs_version String refine_viral_assemble_version = refine.viral_assemble_version } }

WORKFLOW scaffold_and_refine

Imports

Workflow: scaffold_and_refine

Inputs

Outputs

Calls

CALL TASKS scaffold ↗

CALL WORKFLOW refine ↗ → assemble_refbased

Images

scaffold_and_refine - Workflow Graph

scaffold_and_refine - WDL Source Code

CALL TASKS `scaffold` ↗

CALL WORKFLOW `refine` ↗ → assemble_refbased