Skip to content

Commit

Permalink
ensure complete counts report is output to logs dir
Browse files Browse the repository at this point in the history
  • Loading branch information
apriltuesday committed Apr 26, 2024
1 parent 4bbfd8f commit 8c508c3
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 1 deletion.
3 changes: 2 additions & 1 deletion cmat/output_generation/report.py
Original file line number Diff line number Diff line change
Expand Up @@ -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}
Expand Down
2 changes: 2 additions & 0 deletions pipelines/annotation_pipeline.nf
Original file line number Diff line number Diff line change
Expand Up @@ -385,6 +385,8 @@ process generateEvidence {
process collectEvidenceStrings {
label 'short_time'
label 'small_mem'
clusterOptions "-o ${batchRoot}/logs/collect_counts.out \
-e ${batchRoot}/logs/collect_counts.err"

publishDir "${batchRoot}/evidence_strings",
overwrite: true,
Expand Down

0 comments on commit 8c508c3

Please sign in to comment.