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When checking the accessioning QC we do not need to count star * allele #229

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merged 6 commits into from
Nov 14, 2024
Merged

When checking the accessioning QC we do not need to count star * allele #229

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ef4c750
When checking the accessioning QC we do not need to count star * allele
tcezard Nov 6, 2024
dba5fc7
Ensure grep is not the last command because it exit with 1 when nothi…
tcezard Nov 7, 2024
709a066
Always exit the java command with 0
tcezard Nov 7, 2024
8981273
update the comment
tcezard Nov 7, 2024
c829973
Keep the java exit code to check if successful and only check the QC …
tcezard Nov 13, 2024
78563dc
fix typo
tcezard Nov 13, 2024
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23 changes: 18 additions & 5 deletions eva_submission/nextflow/accession_and_load.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -236,14 +236,27 @@ process accession_vcf {


"""
(java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || \
(java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || java_exit_code=\$?
# need this line to ensure we do not get unbound variable when the java process is successful
if [ \${java_exit_code:-"Not set"} == "Not set" ]; then java_exit_code=0; fi
# 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
# 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) ]]

grep -oP '\\d+(?= unaccessioned variants need to be checked)' ${params.logs_dir}/${log_filename}.log || grep_exit_code=\$?
if [ \${grep_exit_code:-"Not set"} == "Not set" ]; then grep_exit_code=0; fi

# 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 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 "java_exit_code \$java_exit_code"
echo "grep_exit_code \$grep_exit_code"
echo "SV_IN_ACCESSION \$SV_IN_ACCESSION"
echo "SV_IN_QC_REPORT \$SV_IN_QC_REPORT"
# If the java is successful OR QC reports missing variants (only valid reason for failure) and QC has the same number of skipped variant as the accession
[[ \$java_exit_code == 0 ]] || ([[ \$grep_exit_code == 0 ]] && [[ \$SV_IN_ACCESSION == \$SV_IN_QC_REPORT ]])
echo "done" > ${accessioned_filename}.tmp
"""
}
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