more scaffolding updates

pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl

@@ -1,6 +1,7 @@
 version 1.0
 
 import "../tasks/tasks_assembly.wdl" as assembly
+import "../tasks/tasks_metagenomics.wdl" as metagenomics
 import "../tasks/tasks_ncbi.wdl" as ncbi
 import "../tasks/tasks_utils.wdl" as utils
 import "assemble_refbased.wdl" as assemble_refbased
@@ -18,11 +19,23 @@ workflow scaffold_and_refine_multitaxa {
         File    reads_unmapped_bam
 
         File    taxid_to_ref_accessions_tsv
+        File?   focal_report_tsv
+        File?   ncbi_taxdump_tgz
 
         # Float    min_pct_reference_covered = 0.1
     }
 
-    Array[Array[String]] taxid_to_ref_accessions = read_tsv(taxid_to_ref_accessions_tsv)
+    # if kraken reports are available, filter scaffold list to observed hits (output might be empty!)
+    if(defined(focal_report_tsv) && defined(ncbi_taxdump_tgz)) {
+        call metagenomics.filter_refs_to_found_taxa {
+            input:
+                taxid_to_ref_accessions_tsv = taxid_to_ref_accessions_tsv,
+                taxdump_tgz = select_first([ncbi_taxdump_tgz]),
+                focal_report_tsv = select_first([focal_report_tsv])
+        }
+    }
+
+    Array[Array[String]] taxid_to_ref_accessions = read_tsv(select_first([filter_refs_to_found_taxa.filtered_taxid_to_ref_accessions_tsv, taxid_to_ref_accessions_tsv]))
     Array[String] assembly_header = ["sample_id", "taxid", "tax_name", "assembly_fasta", "aligned_only_reads_bam", "coverage_plot", "assembly_length", "assembly_length_unambiguous", "reads_aligned", "mean_coverage", "percent_reference_covered", "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"]
 
     scatter(taxon in taxid_to_ref_accessions) {
@@ -51,8 +64,8 @@ workflow scaffold_and_refine_multitaxa {
                 reference_fasta     = scaffold.scaffold_fasta,
                 sample_name         = sample_id
         }
-        # to do: if percent_reference_covered > some threshold, run ncbi.rename_fasta_header and ncbi.align_and_annot_transfer_single
-        # to do: if biosample attributes file provided, run ncbi.biosample_to_genbank
+        # TO DO: if percent_reference_covered > some threshold, run ncbi.rename_fasta_header and ncbi.align_and_annot_transfer_single
+        # TO DO: if biosample attributes file provided, run ncbi.biosample_to_genbank
 
         if (refine.reference_genome_length > 0) {
             Float percent_reference_covered = 1.0 * refine.assembly_length_unambiguous / refine.reference_genome_length
@@ -100,14 +113,10 @@ workflow scaffold_and_refine_multitaxa {
     }
 
     output {
-        Array[Map[String,String]] assembly_stats_by_taxon = stats_by_taxon
-        File   assembly_stats_by_taxon_tsv = concatenate.combined
-
-        Int    num_read_groups                       = refine.num_read_groups[0]
-        Int    num_libraries                         = refine.num_libraries[0]
+        Array[Map[String,String]] assembly_stats_by_taxon  = stats_by_taxon
+        File   assembly_stats_by_taxon_tsv                 = concatenate.combined
+        String assembly_method                             = "viral-ngs/scaffold_and_refine_multitaxa"
 
-        String assembly_method = "viral-ngs/scaffold_and_refine_multitaxa"
-        String scaffold_viral_assemble_version       = scaffold.viralngs_version[0]
-        String refine_viral_assemble_version         = refine.viral_assemble_version[0]
+        # TO DO: some summary stats on stats_by_taxon: how many rows, numbers from the best row, etc
     }
 }