...
Monitor progress of job:
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qjobs |
Preparing “sample sheet” index file:
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#fetch samples names
ls --color=never SRR243020* -1 | awk -F "." '{print $1}' > sample.names
#fetch the path to each FASTQ file
for i in `ls --color=never SRR243020*`; do echo $i; readlink -f $i >> sample.path ; done
#merge the sample names and FASTQ path
echo "sample,fastq1" > samplesheet.csv
paste sample.names sample.path | awk '{print $1 "," $2}' >> samplesheet.csv |