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Verified Commit 2820a500 authored by Laurent Modolo's avatar Laurent Modolo
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gatk4: add vcf indexing for BaseRecalibartor

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src/nf_modules/gatk4/main.nf
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......@@ -125,6 +125,10 @@ process recalibrate_snp_table {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" IndexFeatureFile \
-I ${snp_file}
gatk --java-options "-Xmx${xmx_memory}G" IndexFeatureFile \
-I ${indel_file}
gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
-R ${fasta} \
-I ${bam} \
......
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