Fix failure log expected filename, add needed wdl outputs to short-re…

…ad-mngs postprocess
chanzuckerberg · Feb 10, 2024 · cb549f1 · cb549f1
1 parent 8681e5a
commit cb549f1
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/workflows/amr/run.wdl b/workflows/amr/run.wdl
@@ -643,7 +643,7 @@ task RunSpades {
     output { 
         File contigs = "spades/contigs.fasta"
         File? scaffolds = "spades/scaffolds.fasta"
-        File? failure_log = "spades_failure.tsv"
+        File? failure_log = "spades_failure.json"
     }
     runtime { 
         docker: docker_image_id

diff --git a/workflows/short-read-mngs/postprocess.wdl b/workflows/short-read-mngs/postprocess.wdl
@@ -34,6 +34,7 @@ task RunAssembly {
     File? assembly_spades_output_log = "assembly/spades/spades.log"
     File? output_read_count = "assembly_out.count"
     File? version = "assembly_version.txt"
+    File? failure_log = "spades_failure.json"
   }
   runtime {
     docker: docker_image_id
@@ -680,6 +681,7 @@ workflow czid_postprocess {
     File? assembly_out_assembly_spades_output_log = RunAssembly.assembly_spades_output_log
     File? spades_version = RunAssembly.version
     File? assembly_out_count = RunAssembly.output_read_count
+    File? spades_failure_tracking_log = RunAssembly.failure_log
     File coverage_out_assembly_contig_coverage_json = GenerateCoverageStats.assembly_contig_coverage_json
     File coverage_out_assembly_contig_coverage_summary_csv = GenerateCoverageStats.assembly_contig_coverage_summary_csv
     File? coverage_out_count = GenerateCoverageStats.output_read_count