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Allow accession to complete when there are SV duplicates in the source file #225

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Oct 23, 2024
Merged

Allow accession to complete when there are SV duplicates in the source file #225

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4 changes: 3 additions & 1 deletion eva_submission/nextflow/accession_and_load.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,9 @@ process accession_vcf {
# If accessioning fails due to missing variants, but the only missing variants are structural variants,
# then we should treat this as a success from the perspective of the automation.
# TODO revert once accessioning pipeline properly registers structural variants
[[ \$(grep -o 'Skipped processing structural variant' ${params.logs_dir}/${log_filename}.log | wc -l) \
# First grep finds the "Structural variant" reported by the accessioning process, remove the duplicates and count
# Second grep count the reported number of missing variants in the Accessioning report
[[ \$(grep 'Skipped processing structural variant' ${params.logs_dir}/${log_filename}.log | cut -d ' ' -f 10- | sort -u| wc -l) \
== \$(grep -oP '\\d+(?= unaccessioned variants need to be checked)' ${params.logs_dir}/${log_filename}.log) ]]
echo "done" > ${accessioned_filename}.tmp
"""
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