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biowdl
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eba9ad4c
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eba9ad4c
authored
2 years ago
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Cats
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add some options to disable filters in fastp
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9e946c70
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eba9ad4c
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@@ -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"
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@@ -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 {
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@@ -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"}
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