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Rename sequencing_runs to number_of_reads

This commit is contained in:
coolneng 2021-04-21 20:09:02 +02:00
parent 1020d610d3
commit 2a997a3e5c
Signed by: coolneng
GPG Key ID: 9893DA236405AF57
1 changed files with 3 additions and 3 deletions
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6
generation.sh
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@ -1,7 +1,7 @@
#!/bin/sh #!/bin/sh
usage() { usage() {
echo "usage: generation.sh <number of sequences> <sequencing runs>" echo "usage: generation.sh <number of sequences> <number_of_reads>"
exit 1 exit 1
} }
@ -10,7 +10,7 @@ if [ $# != 2 ]; then
fi fi
sequences=$1 sequences=$1
sequencing_runs=$2 number_of_reads=$2
read_mean_size=350 read_mean_size=350
read_variance_size=0.0 read_variance_size=0.0
data_directory="data/" data_directory="data/"
@ -19,5 +19,5 @@ fastq=".fastq"
filename="sequence" filename="sequence"
prefix="curesim_" prefix="curesim_"
Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n $((sequencing_runs * sequences)) -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq" Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n $((number_of_reads * sequences)) -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
rm "$data_directory/log.txt" rm "$data_directory/log.txt"