Terra/Cromwell doesnt like write_tsv outside of input context

broadinstitute · Sep 19, 2024 · 0915bf5 · 0915bf5
1 parent 034e952
commit 0915bf5
Showing 1 changed file with 10 additions and 4 deletions.
diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
@@ -50,7 +50,6 @@ 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"]
- File assembly_header_tsv = write_tsv([assembly_header])
  scatter(ref_cluster_tar in select_references.matched_reference_clusters_fastas_tars) {
 
  call utils.tar_extract {
@@ -160,16 +159,23 @@ workflow scaffold_and_refine_multitaxa {
 
  ### summary stats
  if (length(select_all(stat_by_taxon)) > 0) {
- call utils.concatenate {
+ call utils.concatenate as assembly_stats_non_empty {
  input:
- infiles = [assembly_header_tsv, write_tsv(select_all(stat_by_taxon))],
+ infiles = [write_tsv([assembly_header]), write_tsv(select_all(stat_by_taxon))],
+ output_name = "assembly_metadata-~{sample_id}.tsv"
+ }
+ }
+ if (length(select_all(stat_by_taxon)) == 0) {
+ call utils.concatenate as assembly_stats_empty {
+ input:
+ infiles = [write_tsv([assembly_header])],
  output_name = "assembly_metadata-~{sample_id}.tsv"
  }
  }
 
  output {
  Array[Map[String,String]] assembly_stats_by_taxon = stats_by_taxon
- File assembly_stats_by_taxon_tsv = select_first([concatenate.combined, assembly_header_tsv])
+ File assembly_stats_by_taxon_tsv = select_first([assembly_stats_non_empty.combined, assembly_stats_empty.combined])
  String assembly_method = "viral-ngs/scaffold_and_refine_multitaxa"
 
  #String assembly_top_taxon_id = select_references.top_matches_per_cluster_basenames[0]