From af73c53935206dd54b37079e1c8d6a5b053c4a46 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Tue, 11 Aug 2020 17:50:15 +0200
Subject: [PATCH] Change inputs to arrays.
---
CHANGELOG.md | 3 ++-
bam2fastx.wdl | 20 ++++++++++----------
2 files changed, 12 insertions(+), 11 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 57bbfec..eb2ef27 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,7 +11,8 @@ that users understand how the changes affect the new version.
version 4.1.0-dev
---------------------------
-+ Remove globs from lima outputs.
++ Bam2fastx: Input bam and index are now arrays.
++ Lima: Remove globs from outputs.
+ Added a task for GRIDSS.
+ Add wdl file for pacbio's bam2fastx tool.
diff --git a/bam2fastx.wdl b/bam2fastx.wdl
index 5e5fb50..a8f1342 100644
--- a/bam2fastx.wdl
+++ b/bam2fastx.wdl
@@ -22,8 +22,8 @@ version 1.0
task Bam2Fasta {
input {
- File inputFile
- File bamIndex
+ Array[File]+ inputFile
+ Array[File]+ bamIndex
String outputPrefix
Int compressionLevel = 1
Boolean splitByBarcode = false
@@ -43,7 +43,7 @@ task Bam2Fasta {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{inputFile}
+ ~{sep=" " inputFile}
}
output {
@@ -58,8 +58,8 @@ 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"}
+ inputFile: {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"}
splitByBarcode: {description: "Split output into multiple fasta files, by barcode pairs.", category: "advanced"}
@@ -75,8 +75,8 @@ task Bam2Fasta {
task Bam2Fastq {
input {
- File inputFile
- File bamIndex
+ Array[File]+ inputFile
+ Array[File]+ bamIndex
String outputPrefix
Int compressionLevel = 1
Boolean splitByBarcode = false
@@ -96,7 +96,7 @@ task Bam2Fastq {
-c ~{compressionLevel} \
~{true="--split-barcodes" false="" splitByBarcode} \
~{"--seqid-prefix " + seqIdPrefix} \
- ~{inputFile}
+ ~{sep=" " inputFile}
}
output {
@@ -111,8 +111,8 @@ 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"}
+ inputFile: {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"}
splitByBarcode: {description: "Split output into multiple fastq files, by barcode pairs.", category: "advanced"}
--
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