From 7bc3c58d309fcb20d9769180f471d79432d2e350 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Mon, 7 Sep 2020 17:26:42 +0200
Subject: [PATCH] make bcftools indexing optional
---
bcftools.wdl | 102 +++++++++++++++++++++++++++------------------------
1 file changed, 54 insertions(+), 48 deletions(-)
diff --git a/bcftools.wdl b/bcftools.wdl
index 520bcf1..5d5a1ea 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -52,6 +52,8 @@ task Annotate {
String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
}
+ Boolean indexing = if outputType == "z" then true else false
+
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
@@ -77,13 +79,14 @@ task Annotate {
~{true="--single-overlaps" false="" singleOverlaps} \
~{true="--remove" false="" length(removeAnns) > 0} ~{sep="," removeAnns} \
~{inputFile}
- bcftools index --tbi ~{outputPath}
+
+ ~{if indexing then 'bcftools index --tbi ~{outputPath}' else ''}
}
output {
File outputVcf = outputPath
- File outputVcfIndex = outputPath + ".tbi"
+ File? outputVcfIndex = outputPath + ".tbi"
}
runtime {
@@ -132,6 +135,8 @@ task Sort {
String outputType = "z"
}
+ Boolean indexing = if outputType == "z" then true else false
+
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
@@ -139,12 +144,13 @@ task Sort {
-o ~{outputPath} \
-O ~{outputType} \
~{inputFile}
- bcftools index --tbi ~{outputPath}
+
+ ~{if indexing then 'bcftools index --tbi ~{outputPath}' else ''}
}
output {
File outputVcf = outputPath
- File outputVcfIndex = outputPath + ".tbi"
+ File? outputVcfIndex = outputPath + ".tbi"
}
runtime {
@@ -165,50 +171,6 @@ task Sort {
}
-task View {
- input {
- File inputFile
- String outputPath = "output.vcf.gz"
- String memory = "256M"
- Int timeMinutes = 1 + ceil(size(inputFile, "G"))
- String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
- String outputType = "z"
- Int compressionLevel = 1
- }
-
- command {
- set -e
- mkdir -p "$(dirname ~{outputPath})"
- bcftools view \
- -o ~{outputPath} \
- -O ~{outputType} \
- -l ~{compressionLevel} \
- ~{inputFile}
- bcftools index --tbi ~{outputPath}
- }
-
- output {
- File outputVcf = outputPath
- File outputVcfIndex = outputPath + ".tbi"
- }
-
- runtime {
- memory: memory
- time_minutes: timeMinutes
- docker: dockerImage
- }
-
- parameter_meta {
- inputFile: {description: "A vcf or bcf file.", category: "required"}
- outputPath: {description: "The location the output VCF file should be written.", category: "common"}
- outputType: {description: "Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf", category: "advanced"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
- compressionLevel: {description: "Compression level from 0 (uncompressed) to 9 (best).", category: "advanced"}
- timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
- dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
- }
-}
-
task Stats {
input {
File inputVcf
@@ -313,3 +275,47 @@ task Stats {
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
}
}
+
+task View {
+ input {
+ File inputFile
+ String outputPath = "output.vcf"
+ Int compressionLevel = 0
+ String memory = "256M"
+ Int timeMinutes = 1 + ceil(size(inputFile, "G"))
+ String dockerImage = "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
+ }
+
+ String outputType = if compressionLevel > 0 then "z" else "v"
+ Boolean indexing = if compressionLevel > 0 then true else false
+
+ command {
+ set -e
+ mkdir -p "$(dirname ~{outputPath})"
+ bcftools view \
+ -o ~{outputPath} \
+ -l ~{compressionLevel} \
+ -O ~{outputType} \
+ ~{inputFile}
+
+ ~{if indexing then 'bcftools index --tbi ~{outputPath}' else ''}
+ }
+ output {
+ File outputVcf = outputPath
+ File? outputVcfIndex = outputPath + ".tbi"
+ }
+
+ runtime {
+ memory: memory
+ time_minutes: timeMinutes
+ docker: dockerImage
+ }
+
+ parameter_meta {
+ inputFile: {description: "A vcf or bcf file.", category: "required"}
+ outputPath: {description: "The location the output VCF file should be written.", category: "common"}
+ 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"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+ }
+}
--
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