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>
---
 workflows/fastq2fasta/bcftools-norm.cwl | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 workflows/fastq2fasta/bcftools-norm.cwl

(limited to 'workflows/fastq2fasta/bcftools-norm.cwl')

diff --git a/workflows/fastq2fasta/bcftools-norm.cwl b/workflows/fastq2fasta/bcftools-norm.cwl
new file mode 100644
index 0000000..a765e65
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-norm.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+  - norm
+  - -Ob
+  - -f
+  - $(inputs.ref_fasta)
+  - -o
+  - $(inputs.output_name)
+  - --threads
+  - $(inputs.threads)
+  - $(inputs.bcf)
+inputs:
+  - id: ref_fasta
+    type: File
+  - id: output_name
+    type: string
+    default: "normalized.bcf"
+  - id: threads
+    type: int
+  - id: bcf
+    type: File
+outputs:
+ - id: normalized_bcf
+   type: File
+   outputBinding:
+     glob: "$(inputs.output_name)"
-- 
cgit v1.2.3