From ac3ee59598026cb22cf40325dbf32b0bc5e988fb Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Thu, 13 Aug 2020 15:17:53 +0200
Subject: [PATCH] Rename input files.
---
bam2fastx.wdl | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index a8f1342..42240cd 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -22,7 +22,7 @@ version 1.0
task Bam2Fasta {
input {
- Array[File]+ inputFile
+ Array[File]+ bam
Array[File]+ bamIndex
String outputPrefix
Int compressionLevel = 1
@@ -43,7 +43,7 @@ task Bam2Fasta {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{sep=" " inputFile}
+ ~{sep=" " bam}
}
output {
@@ -58,7 +58,7 @@ task Bam2Fasta {
parameter_meta {
# inputs
- inputFile: {description: "The input pacbio bam file(s).", category: "required"}
+ bam: {description: "The input pacbio bam file(s).", category: "required"}
bamIndex: {description: "The .pbi index for the input file(s).", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
@@ -75,7 +75,7 @@ task Bam2Fasta {
task Bam2Fastq {
input {
- Array[File]+ inputFile
+ Array[File]+ bam
Array[File]+ bamIndex
String outputPrefix
Int compressionLevel = 1
@@ -96,7 +96,7 @@ task Bam2Fastq {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{sep=" " inputFile}
+ ~{sep=" " bam}
}
output {
@@ -111,7 +111,7 @@ task Bam2Fastq {
parameter_meta {
# inputs
- inputFile: {description: "The input pacbio bam file(s).", category: "required"}
+ bam: {description: "The input pacbio bam file(s).", category: "required"}
bamIndex: {description: "The .pbi index for the input file(s).", category: "required"}
outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
compressionLevel: {description: "Gzip compression level [1-9]", category: "advanced"}
--
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