add warnings to gathered output

theiagen · Oct 21, 2024 · 05d55f7 · 05d55f7
1 parent 166e9fb
commit 05d55f7
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/tasks/utilities/data_handling/task_gather_scatter.wdl b/tasks/utilities/data_handling/task_gather_scatter.wdl
@@ -16,6 +16,8 @@ task gather_scatter {
     File? fastq_scan_docker
     File? fastq_scan_version
     # Assembly 
+    File? metaspades_warning
+    File? pilon_warning
     File? pilon_assembly_fasta### maybe?????
     # quast outputs
     File? quast_genome_length
@@ -92,6 +94,8 @@ task gather_scatter {
     df = load_json_data("~{fastq_scan_num_reads_binned_pairs}", "fastq_scan_num_reads_binned_pairs", df)
     df = load_json_data("~{fastq_scan_docker}", "fastq_scan_docker", df)
     df = load_json_data("~{fastq_scan_version}", "fastq_scan_version", df)
+    df = load_json_data("~{metaspades_warning}", "metaspades_warning", df)
+    df = load_json_data("~{pilon_warning}", "pilon_warning", df)
     df = load_json_data("~{pilon_assembly_fasta}", "pilon_assembly_fasta", df)
     df = load_json_data("~{quast_genome_length}", "quast_genome_length", df)
     df = load_json_data("~{quast_number_contigs}", "quast_number_contigs", df)

diff --git a/workflows/theiameta/wf_theiameta_panel_illumina_pe.wdl b/workflows/theiameta/wf_theiameta_panel_illumina_pe.wdl
@@ -115,14 +115,16 @@ workflow theiameta_panel_illumina_pe {
       samplename = samplename,
       taxon_ids = write_json(taxon_ids),
       organism = write_json(krakentools.organism_name),
-      extracted_read1 = write_json(krakentools.extracted_read1),
+      extracted_read1 = write_json(krakentools.extracted_read1), ## not sure how useful these links are
       extracted_read2 = write_json(krakentools.extracted_read2),
       krakentools_docker = write_json(krakentools.krakentools_docker),
       fastq_scan_num_reads_binned1 = write_json(fastq_scan_binned.read1_seq),
       fastq_scan_num_reads_binned2 = write_json(fastq_scan_binned.read2_seq),
       fastq_scan_num_reads_binned_pairs = write_json(fastq_scan_binned.read_pairs),
       fastq_scan_docker = write_json(fastq_scan_binned.fastq_scan_docker),
       fastq_scan_version = write_json(fastq_scan_binned.version),
+      metaspades_warning = write_json(metaspades_pe.metaspades_warning),
+      pilon_warning = write_json(pilon.pilon_warning),
       pilon_assembly_fasta = write_json(pilon.assembly_fasta), # maybe??
       quast_genome_length = write_json(quast.genome_length),
       quast_number_contigs = write_json(quast.number_contigs),