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Add Random Subsampling to Nanopore mNGS Pipeline #371

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Jun 20, 2024
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Add Random Subsampling to Nanopore mNGS Pipeline #371

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4 changes: 3 additions & 1 deletion workflows/long-read-mngs/run.wdl
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Expand Up @@ -268,7 +268,9 @@ task RunSubsampling {

command <<<
set -euxo pipefail
head -"~{subsample_depth}" "~{input_fastq}" > sample.subsampled.fastq

# set seed to 42 for reproducibility
seqtk sample -s42 "~{input_fastq}" "~{subsample_depth}" > sample.subsampled.fastq

# We should always have reads after subsampling, but adding for consistency with other steps
filter_count sample.subsampled.fastq subsampled "No reads remaining after subsampling"
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