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Verified Commit f167d159 authored by Laurent Modolo's avatar Laurent Modolo
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g2gtools: fix vci_build command

parent 15bb2a0a
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...@@ -13,11 +13,15 @@ process vci_build { ...@@ -13,11 +13,15 @@ process vci_build {
tuple val(file_id), path("*.vci.gz"), emit: vci tuple val(file_id), path("*.vci.gz"), emit: vci
tuple val(file_id), path("*_report.txt"), emit: report tuple val(file_id), path("*_report.txt"), emit: report
script: script:
input_vcf = ""
for (vcf_file in vcf) {
input_vcf += " -i ${vcf_file}"
}
""" """
g2gtools vcf2vci \ g2gtools vcf2vci \
-p ${task.cpus} \ -p ${task.cpus} \
-f ${fasta} \ -f ${fasta} \
-i ${vcf} \ ${input_vcf} \
-s ${file_id} \ -s ${file_id} \
-o ${file_id}.vci.gz 2> ${file_id}_g2gtools_vcf2vci_report.txt -o ${file_id}.vci.gz 2> ${file_id}_g2gtools_vcf2vci_report.txt
""" """
......
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