From d781e42c9adac07253cb928ae66e9b7314710267 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 20 Apr 2020 12:55:18 -0400
Subject: Move workflows into main repo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 .../fastq2fasta/fastq2fasta-create-bwaindex.cwl    | 41 ++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl

(limited to 'workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl')

diff --git a/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
new file mode 100644
index 0000000..dab7ff2
--- /dev/null
+++ b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
@@ -0,0 +1,41 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  SubworkflowFeatureRequirement: {}
+hints:
+  ResourceRequirement:
+    ramMin: 3000
+
+inputs:
+  ref_fasta:
+    type: File
+  fastq_forward:
+    type: File
+  fastq_reverse:
+    type: File?
+  threads:
+    type: int
+    default: 4
+
+outputs:
+  out_fasta:
+    type: File
+    outputSource: fastq2fasta/out_fasta
+
+steps:
+  bwa-index:
+    in: {input_fasta: ref_fasta}
+    out: [indexed_fasta]
+    run: bwa-index.cwl
+  samtools-faidx:
+    in: {input_fasta: bwa-index/indexed_fasta}
+    out: [indexed_fasta]
+    run: samtools-faidx.cwl
+  fastq2fasta:
+    in:
+      fastq_forward: fastq_forward
+      fastq_reverse: fastq_reverse
+      ref_fasta: samtools-faidx/indexed_fasta
+      threads: threads
+    out: [out_fasta]
+    run: fastq2fasta.cwl
-- 
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