From 8fa3c3d13c4ccc05f083d73b907ce3be9f4a0b47 Mon Sep 17 00:00:00 2001 From: April Shen Date: Fri, 26 Apr 2024 12:54:18 +0100 Subject: [PATCH] ensure complete counts report is output to logs dir --- cmat/output_generation/report.py | 3 ++- pipelines/annotation_pipeline.nf | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/cmat/output_generation/report.py b/cmat/output_generation/report.py index f7b404c7..b2403c7b 100644 --- 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 index 3dee5aed..ea8c866e 100644 --- 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,