Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view filter-wrapper.sh @ 6:3c50a937d7c1 draft
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author | bcclaywell |
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date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | 2d023c621bd0 |
children |
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#!/bin/bash source $(dirname $0)/util.sh source $1 INPUT_QUAL=$(extify qual ${INPUT_QUAL}) BARCODES=$(extify csv ${BARCODES}) RAW_SEQS=$(extify fasta ${RAW_SEQS}) seqmagick quality-filter \ --input-qual ${INPUT_QUAL} \ --barcode-file ${BARCODES} \ --primer "${PRIMER}" \ --report-out ${FILTER_REPORT} \ --details-out ${FILTER_DETAILS} \ --map-out ${SPLIT_MAP} \ --barcode-header \ --min-length ${MIN_LENGTH} \ --min-mean-quality ${MIN_QUALITY} \ --quality-window 30 \ --quality-window-prop 0.9 \ --quality-window-mean-qual 15 \ ${RAW_SEQS} \ filtered.fasta if [[ ${REVERSE_COMPLEMENT} == "TRUE" ]]; then seqmagick mogrify \ --reverse-complement \ filtered.fasta fi mv filtered.fasta ${FILTERED_SEQS} sequencing_quality_report.py ${PLATE_JSON} -t "Sequencing quality report" -o ${SQR_DIR} cat <<EOF > ${SQR} <!DOCTYPE HTML> <html lang="en-US"> <head/> <body> <a href="index.html">Sequencing quality report</a> </body> </html> EOF