From abc0884155ef69b9a51f5ac1f88a0c39611d6881 Mon Sep 17 00:00:00 2001 From: Vincent Selhorst-Jones Date: Mon, 24 Jul 2023 12:07:04 -0700 Subject: [PATCH] Clarify TODO comment about fragment lengths --- workflows/short-read-mngs/host_filter.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/workflows/short-read-mngs/host_filter.wdl b/workflows/short-read-mngs/host_filter.wdl index cf622a6a6..ab5a2566e 100644 --- a/workflows/short-read-mngs/host_filter.wdl +++ b/workflows/short-read-mngs/host_filter.wdl @@ -428,7 +428,10 @@ task kallisto { Int cpu = 16 } Boolean paired = defined(fastp2_fastq) - # TODO: input fragment length parameters for non-paired-end (l = average, s = std dev) + # TODO: It would be better to have fragment length params for non-paired-end + # (l = average, s = std dev) get set dynamically based on the input data. + # See this GitHub comment for more background info: + # https://github.com/chanzuckerberg/czid-workflows/pull/282#issuecomment-1647494061 String kallisto_invocation = "/kallisto/kallisto quant" + " -i '${kallisto_idx}' -o $(pwd) --plaintext ${if (paired) then '' else '--single -l 200 -s 20'} ${kallisto_options}" + " '~{fastp1_fastq}'" + if (defined(fastp2_fastq)) then " '~{fastp2_fastq}'" else ""