Merge pull request #426 from apriltuesday/june-submission

Ensure complete counts report is output to logs dir
EBIvariation · Apr 30, 2024 · b9cdaa0 · b9cdaa0
2 parents 4bbfd8f + 27ce9be
commit b9cdaa0
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/OT_SCHEMA_VERSION b/OT_SCHEMA_VERSION
@@ -1 +1 @@
-2.7.0
+2.7.1
diff --git a/cmat/output_generation/report.py b/cmat/output_generation/report.py
@@ -110,7 +110,8 @@ def print_report(self):
             Total number of complete evidence strings generated\t{self.complete_evidence_string_count}
 
             Total number of ClinVar records\t{self.clinvar_total}
-                Fatal: No traits with valid names\t{self.clinvar_fatal_no_valid_traits}
+                Fatal: Cannot produce evidence\t{self.clinvar_fatal}
+                    No traits with valid names\t{self.clinvar_fatal_no_valid_traits}
                     No clinical significance\t{self.clinvar_fatal_no_clinical_significance}
                 Skipped: Can be rescued by future improvements\t{self.clinvar_skipped}
                     Unsupported variation type\t{self.clinvar_skip_unsupported_variation}

diff --git a/pipelines/annotation_pipeline.nf b/pipelines/annotation_pipeline.nf
@@ -409,6 +409,8 @@ process collectEvidenceStrings {
 process collectCounts {
     label 'short_time'
     label 'small_mem'
+    clusterOptions "-o ${batchRoot}/logs/collect_counts.out \
+                    -e ${batchRoot}/logs/collect_counts.err"
 
     publishDir "${batchRoot}/logs",
         overwrite: true,