New version of ParseDarwinSamplesheet.sh script, finetuning concordance.sh, changed log location, lost of bugfixes #38
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…winSamplesheet.sh as Jobfile parser.
bin/ParseDarwinSamplesheet.sh
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| local _prefix="" | ||
| _prefix=$(echo "${_project}" | awk -F '_' '{print $1}') | ||
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| if [[ "${_prefix}" =~ ^(NGS|NGSR|QXTR|XHTS|MAGR|QXT|HSR|GS)$ ]] && [[ "${_type}" =~ ^(WES|WGS )$ ]] |
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^(WES|WGS )$
is die ruimte bewust gekozen?
bin/ParseDarwinSamplesheet.sh
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| #kolom 1: processStepID | ||
| #kolom 2: projectNaam 1 | ||
| #kolom 3: DNA nummer 2 |
| #check if reheadering is needed. | ||
| sampleName=$(bcftools query -l "!{sampleId}.called.sorted.vcf.gz") | ||
| if [[ ${sampleName} != !{sampleId} ]] |
RoanKanninga
approved these changes
Jul 19, 2024
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