From aea639c83bc4b306df01986f55f4e774208e8a8e Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 10 Aug 2020 11:27:23 +0200
Subject: [PATCH] Add index input to the tasks.
---
bam2fastx.wdl | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 21f1c60..27ed15c 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -23,6 +23,7 @@ version 1.0
task Bam2Fasta {
input {
File inputFile
+ File bamIndex
String outputPrefix
Int compressionLevel = 1
Boolean uncompressedOutput = false
@@ -60,6 +61,7 @@ task Bam2Fasta {
parameter_meta {
# inputs
inputFile: {description: "The input pacbio bam file.", category: "required"}
+ bamIndex: {description: "The .pbi index for the input file.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
uncompressedOutput: {description: "Do not compress. In this case, we will not add .gz, and we ignore any -c setting.", category: "advanced"}
@@ -77,6 +79,7 @@ task Bam2Fasta {
task Bam2Fastq {
input {
File inputFile
+ File bamIndex
String outputPrefix
Int compressionLevel = 1
Boolean uncompressedOutput = false
@@ -114,6 +117,7 @@ task Bam2Fastq {
parameter_meta {
# inputs
inputFile: {description: "The input pacbio bam file.", category: "required"}
+ bamIndex: {description: "The .pbi index for the input file.", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
uncompressedOutput: {description: "Do not compress. In this case, we will not add .gz, and we ignore any -c setting.", category: "advanced"}
--
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