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Merge pull request #422 from broadinstitute/dp-denovo-update
incorporate assemble_refbased as refine/polish for denovo
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@@ -7,6 +7,7 @@ workflow align_and_count_report { | |
| description: "Align reads to reference with minimap2 and count the number of hits. Results are returned in the format of 'samtools idxstats'." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| call reports.align_and_count | ||
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@@ -7,6 +7,7 @@ workflow align_and_count_multiple_report { | |
| description: "Count the number of times reads map to provided reference sequences. Useful for counting spike-ins, etc." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
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@@ -8,6 +8,7 @@ workflow align_and_plot { | |
| description: "Align reads to reference and produce coverage plots and statistics." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| call assembly.align_reads as align | ||
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@@ -3,10 +3,17 @@ version 1.0 | |
| import "../tasks/tasks_taxon_filter.wdl" as taxon_filter | ||
| import "../tasks/tasks_read_utils.wdl" as read_utils | ||
| import "../tasks/tasks_assembly.wdl" as assembly | ||
| import "../tasks/tasks_intrahost.wdl" as intrahost | ||
| import "assemble_refbased.wdl" as assemble_refbased | ||
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| workflow assemble_denovo { | ||
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| meta { | ||
| description: "Assisted de novo viral genome assembly from raw reads." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
| File reads_unmapped_bam | ||
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@@ -19,18 +26,7 @@ workflow assemble_denovo { | |
| File? filter_to_taxon_db | ||
| File trim_clip_db | ||
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| File? novocraft_license | ||
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| Boolean call_isnvs=false | ||
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| String assembler="spades" | ||
| Float? scaffold_min_length_fraction | ||
| Float? scaffold_min_unambig | ||
| Int? scaffold_replace_length=55 | ||
| Int? nucmer_max_gap | ||
| Int? nucmer_min_match | ||
| Int? nucmer_min_cluster | ||
| Float? scaffold_min_pct_contig_aligned | ||
| String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned") | ||
| } | ||
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| parameter_meta { | ||
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@@ -57,8 +53,6 @@ workflow assemble_denovo { | |
| } | ||
| } | ||
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| String sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned") | ||
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| if(length(deplete_bmtaggerDbs) + length(deplete_blastDbs) + length(deplete_bwaDbs) > 0) { | ||
| call taxon_filter.deplete_taxa { | ||
| input: | ||
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@@ -87,48 +81,31 @@ workflow assemble_denovo { | |
| reads_unmapped_bam = rmdup_ubam.dedup_bam, | ||
| trim_clip_db = trim_clip_db, | ||
| always_succeed = true, | ||
| assembler = assembler, | ||
| sample_name = sample_name | ||
| } | ||
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| call assembly.scaffold { | ||
| input: | ||
| contigs_fasta = assemble.contigs_fasta, | ||
| reads_bam = select_first([filter_to_taxon.taxfilt_bam, deplete_taxa.cleaned_bam, reads_unmapped_bam]), | ||
| reference_genome_fasta = reference_genome_fasta, | ||
| min_length_fraction = scaffold_min_length_fraction, | ||
| min_unambig = scaffold_min_unambig, | ||
| replace_length = scaffold_replace_length, | ||
| nucmer_max_gap = nucmer_max_gap, | ||
| nucmer_min_match = nucmer_min_match, | ||
| nucmer_min_cluster = nucmer_min_cluster, | ||
| scaffold_min_pct_contig_aligned = scaffold_min_pct_contig_aligned | ||
| } | ||
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| call assembly.refine_2x_and_plot { | ||
| input: | ||
| assembly_fasta = scaffold.scaffold_fasta, | ||
| reads_unmapped_bam = select_first([deplete_taxa.cleaned_bam, reads_unmapped_bam]), | ||
| novocraft_license = novocraft_license, | ||
| sample_name = sample_name | ||
| contigs_fasta = assemble.contigs_fasta, | ||
| reads_bam = select_first([filter_to_taxon.taxfilt_bam, deplete_taxa.cleaned_bam, reads_unmapped_bam]), | ||
| reference_genome_fasta = reference_genome_fasta | ||
| } | ||
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| if(call_isnvs) { | ||
| call intrahost.isnvs_per_sample { | ||
| input: | ||
| assembly_fasta = refine_2x_and_plot.final_assembly_fasta, | ||
| mapped_bam = refine_2x_and_plot.aligned_bam | ||
| } | ||
| call assemble_refbased.assemble_refbased as refine { | ||
| input: | ||
| reads_unmapped_bams = [rmdup_ubam.dedup_bam], | ||
| reference_fasta = scaffold.scaffold_fasta, | ||
| sample_name = sample_name | ||
| } | ||
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| output { | ||
| File final_assembly_fasta = refine_2x_and_plot.final_assembly_fasta | ||
| File aligned_only_reads_bam = refine_2x_and_plot.aligned_only_reads_bam | ||
| File coverage_plot = refine_2x_and_plot.coverage_plot | ||
| Int assembly_length = refine_2x_and_plot.assembly_length | ||
| Int assembly_length_unambiguous = refine_2x_and_plot.assembly_length_unambiguous | ||
| Int reads_aligned = refine_2x_and_plot.reads_aligned | ||
| Float mean_coverage = refine_2x_and_plot.mean_coverage | ||
| 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 | ||
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| File cleaned_bam = select_first([deplete_taxa.cleaned_bam, reads_unmapped_bam]) | ||
| File? cleaned_fastqc = deplete_taxa.cleaned_fastqc | ||
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@@ -155,22 +132,25 @@ workflow assemble_denovo { | |
| String scaffolding_chosen_ref_name = scaffold.scaffolding_chosen_ref_name | ||
| File scaffolding_stats = scaffold.scaffolding_stats | ||
| File scaffolding_alt_contigs = scaffold.scaffolding_alt_contigs | ||
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| 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 | ||
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| File isnvs_vcf = refine.align_to_self_isnvs_vcf | ||
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| File? isnvsFile = isnvs_per_sample.isnvsFile | ||
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| File aligned_bam = refine_2x_and_plot.aligned_bam | ||
| File aligned_only_reads_bam_idx = refine_2x_and_plot.aligned_only_reads_bam_idx | ||
| File aligned_only_reads_fastqc = refine_2x_and_plot.aligned_only_reads_fastqc | ||
| File coverage_tsv = refine_2x_and_plot.coverage_tsv | ||
| Int read_pairs_aligned = refine_2x_and_plot.read_pairs_aligned | ||
| Float bases_aligned = refine_2x_and_plot.bases_aligned | ||
| File aligned_bam = refine.align_to_self_merged_aligned_and_unaligned_bam[0] | ||
| File aligned_only_reads_fastqc = refine.align_to_ref_per_input_fastqc[0] | ||
| 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 | ||
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| String? deplete_viral_classify_version = deplete_taxa.viralngs_version | ||
| String? taxfilt_viral_classify_version = filter_to_taxon.viralngs_version | ||
| String assemble_viral_assemble_version = assemble.viralngs_version | ||
| String scaffold_viral_assemble_version = scaffold.viralngs_version | ||
| String refine_viral_assemble_version = refine_2x_and_plot.viralngs_version | ||
| String? isnvs_viral_phylo_version = isnvs_per_sample.viralngs_version | ||
| } | ||
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| } | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -7,6 +7,7 @@ workflow classify_kraken2 { | |
| description: "Taxonomic classification of sequences via kraken2 (or kraken2x, depending on the database provided)." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| call metagenomics.kraken2 | ||
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@@ -11,6 +11,7 @@ workflow classify_single { | |
| description: "Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
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@@ -8,6 +8,7 @@ workflow demux_only { | |
| description: "Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
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@@ -12,6 +12,7 @@ workflow demux_plus { | |
| description: "Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by basic metagenomics and QC metrics. Intended for automatic triggering post upload on DNAnexus." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -7,6 +7,7 @@ workflow fastq_to_ubam { | |
| description: "Convert reads from fastq format (single or paired) to unaligned BAM format." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| call tasks_read_utils.FastqToUBAM | ||
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@@ -7,6 +7,7 @@ workflow fetch_sra_to_bam { | |
| description: "Retrieve reads from the NCBI Short Read Archive in unaligned BAM format with relevant metadata encoded." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| call ncbi_tools.Fetch_SRA_to_BAM | ||
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@@ -9,6 +9,7 @@ workflow genbank { | |
| description: "Prepare assemblies for Genbank submission. This includes annotation by simple coordinate transfer from Genbank annotations and a multiple alignment. See https://viral-pipelines.readthedocs.io/en/latest/ncbi_submission.html for details." | ||
| author: "Broad Viral Genomics" | ||
| email: "[email protected]" | ||
| allowNestedInputs: true | ||
| } | ||
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| input { | ||
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