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code assumes already-pear'd data are in a single library

Open invertdna opened this issue 9 years ago • 0 comments

when running the pipeline on a multi-library dataset, the current code fails when the "already peared?" option is set to YES, because the script looks for a single merged.assembled.fasta file. This is easily fixed by changing PEAR_OUTPUT='/Users/folderContainingSubfoldersWithLibraryNames' in the params file, and in the main banzai script: line 266 to MERGED_READS="${PEAR_OUTPUT}/$(basename $LIB_OUTPUT_DIR)"/1_merged.assembled.fastq.gz

and line 313 to FILTERED_OUTPUT="${LIB_OUTPUT_DIR%.*}"/1_merged.assembled.fasta

invertdna avatar Jul 20 '16 19:07 invertdna