From 4f0e06930bac0cc0ecbb913547b42db911300b75 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Wed, 8 Jan 2025 13:27:51 -0500 Subject: [PATCH] add a couple columns to table --- pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl index 0af33b228..bfd1d2c1d 100644 --- a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl +++ b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl @@ -21,6 +21,8 @@ workflow scaffold_and_refine_multitaxa { File contigs_fasta File taxid_to_ref_accessions_tsv + + String? biosample_accession } Int min_scaffold_unambig = 10 # in base-pairs; any scaffolded assembly < this length will not be refined/polished @@ -49,7 +51,7 @@ workflow scaffold_and_refine_multitaxa { } # assemble and produce stats for every reference cluster - Array[String] assembly_header = ["entity:assembly_id", "assembly_name", "sample_id", "sample_name", "taxid", "tax_name", "assembly_fasta", "aligned_only_reads_bam", "coverage_plot", "assembly_length", "assembly_length_unambiguous", "reads_aligned", "mean_coverage", "percent_reference_covered", "scaffolding_num_segments_recovered", "reference_num_segments_required", "reference_length", "reference_accessions", "skani_num_ref_clusters", "skani_this_cluster_num_refs", "skani_dist_tsv", "scaffolding_ani", "scaffolding_pct_ref_cov", "intermediate_gapfill_fasta", "assembly_preimpute_length_unambiguous", "replicate_concordant_sites", "replicate_discordant_snps", "replicate_discordant_indels", "replicate_discordant_vcf", "isnvsFile", "aligned_bam", "coverage_tsv", "read_pairs_aligned", "bases_aligned", "coverage_genbank", "assembly_method", "sample"] + Array[String] assembly_header = ["entity:assembly_id", "assembly_name", "sample_id", "sample_name", "taxid", "tax_name", "assembly_fasta", "aligned_only_reads_bam", "coverage_plot", "assembly_length", "assembly_length_unambiguous", "reads_aligned", "mean_coverage", "percent_reference_covered", "scaffolding_num_segments_recovered", "reference_num_segments_required", "reference_length", "reference_accessions", "skani_num_ref_clusters", "skani_this_cluster_num_refs", "skani_dist_tsv", "scaffolding_ani", "scaffolding_pct_ref_cov", "intermediate_gapfill_fasta", "assembly_preimpute_length_unambiguous", "replicate_concordant_sites", "replicate_discordant_snps", "replicate_discordant_indels", "replicate_discordant_vcf", "isnvsFile", "aligned_bam", "coverage_tsv", "read_pairs_aligned", "bases_aligned", "coverage_genbank", "assembly_method", "assembly_method_version", "biosample_accession", "sample"] scatter(ref_cluster_tar in select_references.matched_reference_clusters_fastas_tars) { call utils.tar_extract { @@ -145,7 +147,10 @@ workflow scaffold_and_refine_multitaxa { "bases_aligned" : select_first([refine.align_to_self_merged_bases_aligned, "0"]), "coverage_genbank" : select_first([coverage_two_col.out_tsv, ""]), - "assembly_method" : "viral-ngs/assemble_denovo", + "assembly_method" : "viral-ngs/assemble_denovo", + "assembly_method_version" : scaffold.viralngs_version, + + "biosample_accession" : select_first([biosample_accession, ""]), "sample": '{"entityType":"sample","entityName":"' + sample_id + '"}' }