From 20dd0ab38e31923ea6b46b1beff64c73abc82c94 Mon Sep 17 00:00:00 2001 From: Ash O'Farrell Date: Tue, 12 Nov 2024 11:26:15 -0800 Subject: [PATCH] Add a low-resource mode --- myco_raw.wdl | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/myco_raw.wdl b/myco_raw.wdl index dbaf2d5..16b7d15 100644 --- a/myco_raw.wdl +++ b/myco_raw.wdl @@ -15,6 +15,7 @@ workflow myco { String? output_sample_name Boolean guardrail_mode = true + Boolean low_resource_mode = false Boolean clean_after_decontam = false Int clean_average_q_score = 29 @@ -75,7 +76,9 @@ workflow myco { preliminary_min_q30 = if guardrail_mode then 0.2 else 0.0000001, subsample_cutoff = if guardrail_mode then 30000 else -1, timeout_map_reads = if guardrail_mode then 300 else 0, - timeout_decontam = if guardrail_mode then 600 else 0 + timeout_decontam = if guardrail_mode then 600 else 0, + addldisk = if low_resource_mode then 10 else 100, + memory = if low_resource_mode then 8 else 32 } if(defined(decontam_each_sample.decontaminated_fastq_1)) { @@ -104,7 +107,10 @@ workflow myco { input: reads_files = [real_decontaminated_fastq_1, real_decontaminated_fastq_2], tarball_bams_and_bais = false, - timeout = if guardrail_mode then 600 else 0 + timeout = if guardrail_mode then 600 else 0, + addldisk = if low_resource_mode then 10 else 100, + cpu = if low_resource_mode then 8 else 16, + memory = if low_resource_mode then 8 else 32 } } }