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wshuai294 / PStrain

Pstrain profiles strains in metagenomics data. It infers strain abundance and genotype for each species. Also, it has a single species mode; where given a BAM and VCF, it can phase the variants for any species.
MIT License
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A snippet offering a for-loop based config construction script #8

Closed ctseto closed 1 year ago

ctseto commented 3 years ago

With input fastq in a root directory, in individual folders for each sample, and runs named $sample_1.fastq and $sample_2.fastq, and the names are assigned to a variable, $AllSamples

for I in $AllSamples; do echo "//";echo sample : $I ; echo fq1: /rootdir/$I/$I_1.fastq ; echo fq2: /rootdir/$I/$I_2.fastq ; done

wshuai294 commented 3 years ago

Thank you for your useful script.