Major changes to dataflow of the pipeline, cram/bam support, extra logging to automated #36
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RoanKanninga
previously approved these changes
Apr 25, 2024
bin/ConcordanceCheck-nf.sh
Outdated
| @@ -175,61 +175,110 @@ concordanceDir="/groups/${GROUP}/${TMP_LFS}/concordance/" | |||
| while IFS= read -r sampleSheet | |||
| do | |||
| log4Bash 'INFO' "${LINENO}" "${FUNCNAME:-main}" '0' "Processing samplesheet ${sampleSheet} ..." | |||
| concordanceCheckId=$(basename "${sampleSheet}" .sampleId.txt) | |||
| filePrefix="$(basename "${sampleSheet}" .sampleId.txt)" | |||
| concordanceCheckId=${filePrefix} | |||
RoanKanninga
approved these changes
Apr 26, 2024
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