update tsv header for table names that are non-default

Author: dpark01

pipes/WDL/workflows/assemble_denovo_metagenomic.wdl

@@ -164,7 +164,7 @@ workflow assemble_denovo_metagenomic {
     }
 
     # assemble and produce stats for every reference cluster
-    Array[String] assembly_header = ["entity:assembly_id", "assembly_name", "sample_id", "sample_name", "taxid", "tax_name", "tax_shortname", "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", "assembly_method", "assembly_method_version", "biosample_accession", "batch_ids", "sample"]
+    Array[String] assembly_header = ["entity:assembly_id", "assembly_name", "sample_id", "sample_name", "taxid", "tax_name", "tax_shortname", "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", "assembly_method", "assembly_method_version", "biosample_accession", "batch_ids", "~{table_name}"]
     scatter(ref_cluster_tar in select_references.matched_reference_clusters_fastas_tars) {
 
         call utils.tar_extract {

pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl

@@ -43,7 +43,7 @@ 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", "tax_shortname", "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", "assembly_method", "assembly_method_version", "biosample_accession", "sample"]
+    Array[String] assembly_header = ["entity:assembly_id", "assembly_name", "sample_id", "sample_name", "taxid", "tax_name", "tax_shortname", "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", "assembly_method", "assembly_method_version", "biosample_accession", "~{table_name}"]
     scatter(ref_cluster_tar in select_references.matched_reference_clusters_fastas_tars) {
 
         call utils.tar_extract {