defend against empty input

broadinstitute · Feb 6, 2025 · de73651 · de73651
1 parent 0208be8
commit de73651
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Showing 2 changed files with 14 additions and 6 deletions.
diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
@@ -295,15 +295,22 @@ task coverage_report {
   Int disk_size = 375
 
   command <<<
+    set -e
     reports.py --version | tee VERSION
-    reports.py coverage_only \
-      ~{sep=' ' mapped_bams} \
-      "~{out_report_name}" \
-      --loglevel DEBUG
+    python3 << CODE
+    import tools.samtools
+    import reports
+    in_bams = list([bam for bam in ["~{sep='", "' mapped_bams}"] if bam and not tools.samtools.isEmpty(bam)])
+    if in_bams:
+      reports.coverage_only(in_bams, "~{out_report_name}")
+    else:
+      with open("~{out_report_name}", "w") as outf:
+        outf.write('\t'.join(('sample', 'aln2self_cov_median', 'aln2self_cov_mean', 'aln2self_cov_mean_non0', 'aln2self_cov_1X', 'aln2self_cov_5X', 'aln2self_cov_20X', 'aln2self_cov_100X'))+'\n')
+    CODE
   >>>
 
   output {
-    File   coverage_report  = "~{out_report_name}"
+    File   coverage_report  = out_report_name
     String viralngs_version = read_string("VERSION")
   }
 

diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
@@ -81,7 +81,8 @@ workflow scaffold_and_refine_multitaxa {
             call reports.coverage_report as coverage_self {
                 input:
                     mapped_bams = [refine.align_to_self_merged_aligned_only_bam],
-                    mapped_bam_idx = []
+                    mapped_bam_idx = [],
+                    out_report_name = "~{sample_id}.coverage_report.txt"
             }
             call utils.tsv_drop_cols as coverage_two_col {
                 input: