From 5168c629fd0bfc6ff4632ad090257db85fb85a3d Mon Sep 17 00:00:00 2001 From: Andrew Thrasher Date: Fri, 3 Jan 2025 13:40:03 -0500 Subject: [PATCH] chore: remove memory mapped IO --- tools/bowtie2.wdl | 3 --- 1 file changed, 3 deletions(-) diff --git a/tools/bowtie2.wdl b/tools/bowtie2.wdl index c15e8271..5bff505b 100644 --- a/tools/bowtie2.wdl +++ b/tools/bowtie2.wdl @@ -185,7 +185,6 @@ task align { description: "Force SAM output order to match order of input reads", help: "Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when `ncpu` is set greater than 1. Specifying `reorder` and setting `ncpu` greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory than if `reorder` were not specified. Has no effect if `ncpu` is set to 1, since output order will naturally correspond to input order in that case.", } - memory_map: "use memory-mapped I/O for index; many 'bowtie's can share" qc_filter: { description: "Filter out reads that are bad according to QSEQ filter. Only has an effect when read format is --qseq.", common: false, @@ -266,7 +265,6 @@ task align { Boolean soft_clipped_unmapped_tlen = false Boolean sam_append_comment = false Boolean reorder = false - Boolean memory_map = false Boolean qc_filter = false Int trim5 = 0 Int trim3 = 0 @@ -371,7 +369,6 @@ task align { ~{if defined(sam_opt_config) then "--sam-opt ~{sam_opt_config}" else ""} \ -p ~{ncpu} \ ~{if reorder then "--reorder" else ""} \ - ~{if memory_map then "--mm" else ""} \ ~{if qc_filter then "--qc-filter" else ""} \ --seed ~{seed} \ ~{if non_deterministic then "--non-deterministic" else ""} \