From eba9ad4c057cf7468bd7982930af484765d1a257 Mon Sep 17 00:00:00 2001 From: DavyCats Date: Thu, 23 Feb 2023 15:55:01 +0100 Subject: [PATCH] add some options to disable filters in fastp --- fastp.wdl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/fastp.wdl b/fastp.wdl index db4a2d40..68c0e5cd 100644 --- a/fastp.wdl +++ b/fastp.wdl @@ -36,6 +36,8 @@ task Fastp { Int lengthRequired = 15 Int? split Boolean performAdapterTrimming = true + Boolean performQualityFiltering = true + Boolean performLengthFiltering = true Int threads = 4 String memory = "50GiB" @@ -73,7 +75,9 @@ task Fastp { --thread ~{select_first([effectiveSplit, threads])} \ ~{"--split " + effectiveSplit} \ ~{if defined(effectiveSplit) then "-d 0" else ""} \ - ~{if performAdapterTrimming then "" else "--disable_adapter_trimming"} + ~{if performAdapterTrimming then "" else "--disable_adapter_trimming"} \ + ~{if performQualityFiltering then "" else "--disable_quality_filtering"} \ + ~{if performLengthFiltering then "" else "--disable_length_filtering"} >>> output { @@ -102,6 +106,8 @@ task Fastp { lengthRequired: {description: "The minimum read length.", category: "advanced"} split: {description: "The number of chunks to split the files into. Number of threads will be set equal to the amount of splits.", category: "common"} performAdapterTrimming: {description: "Whether adapter trimming should be performed or not.", category: "advanced"} + performQualityFiltering: {description: "Whether reads should be filtered based on quality scores.", category: "advanced"} + performLengthFiltering: {description: "Whether reads shoulde be filtered based on lengths.", catgegory: "advanced"} threads: {description: "The number of threads to use. Only used if the split input is not set.", category: "advanced"} memory: {description: "The amount of memory this job will use.", category: "advanced"} timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}