11 lines
301 B
Bash
11 lines
301 B
Bash
#!/bin/sh
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SIZE=1
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if [ "$#" -eq 1 ]; then
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SIZE=$1
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fi
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cp samplesheet${SIZE}.csv /workspace/launch/samplesheet.csv
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cp *.fastq.gz /workspace/launch/.
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time nextflow run -c nextflow.config nf-core/sarek -r 3.9.0 -profile docker --genome GRCm38 --input samplesheet.csv --outdir out --skip_tools multiqc
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