diff --git a/bash/lsf_bioinfo_utils.sh b/bash/lsf_bioinfo_utils.sh new file mode 100644 index 0000000000000000000000000000000000000000..31e518ad4bdefbc5a3f6d164415fc602f53b215f --- /dev/null +++ b/bash/lsf_bioinfo_utils.sh @@ -0,0 +1,19 @@ + +mmFastqc(){ + outputDir="fastqc_reports" +# filePattern="fastq.gz" +# outputDir=$1 +# filePattern=$2 + mkdir $outputDir + for fastqFile in *fastq *fastq.gz ; do + if [ ! -f $fastqFile ]; then + continue; + fi + echo processing $fastqFile +# bsub -q medium --J fastqc_$(basename $fastqFile) "fastqc -j /sw/bin/java -o $outputDir -f fastq $fastqFile" | joblist .fastqc_jobs + mysub "fastqc__$(basename $fastqFile)" "fastqc -j /sw/bin/java -o $outputDir -f fastq $fastqFile" -q medium | joblist .fastqc_jobs + done + wait4jobs .fastqc_jobs +} +export -f mmFastqc +