From 89812739662daeb773d5bb92d2024f4a512aa2da Mon Sep 17 00:00:00 2001 From: tcezard Date: Thu, 7 Nov 2024 11:22:46 +0000 Subject: [PATCH] update the comment --- eva_submission/nextflow/accession_and_load.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eva_submission/nextflow/accession_and_load.nf b/eva_submission/nextflow/accession_and_load.nf index 407a21f..6d807af 100644 --- a/eva_submission/nextflow/accession_and_load.nf +++ b/eva_submission/nextflow/accession_and_load.nf @@ -242,7 +242,7 @@ process accession_vcf { # TODO revert once accessioning pipeline properly registers structural variants # First grep finds the "Structural variant" reported by the accessioning process, remove the duplicates, remove the * alleles and count SV_IN_ACCESSION=\$(grep 'Skipped processing structural variant' ${params.logs_dir}/${log_filename}.log | grep -v "alternate='*'" | cut -d ' ' -f 10- | sort -u | wc -l) - # Second grep count the reported number of missing variants in the Accessioning report + # Second grep count the number of missing variants in the Accessioning report after removing the * alleles SV_IN_QC_REPORT=\$(grep ' variants that were not found in the accession report' ${params.logs_dir}/${log_filename}.log | sed 's/, AbstractVariant/\\n AbstractVariant/g' | grep -v "alternate='*'" | wc -l) echo "SV_IN_ACCESSION \$SV_IN_ACCESSION" echo "SV_IN_QC_REPORT \$SV_IN_QC_REPORT"