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/freebayes.cwl | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 workflows/fastq2fasta/freebayes.cwl

(limited to 'workflows/fastq2fasta/freebayes.cwl')

diff --git a/workflows/fastq2fasta/freebayes.cwl b/workflows/fastq2fasta/freebayes.cwl
new file mode 100644
index 0000000..1bf9b2f
--- /dev/null
+++ b/workflows/fastq2fasta/freebayes.cwl
@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+  DockerRequirement:
+    dockerPull: "quay.io/biocontainers/freebayes:1.3.2--py37hc088bd4_0"
+baseCommand: freebayes
+arguments: [
+  --bam, $(inputs.bam),
+  # --region=$(inputs.contig):1-$(inputs.contig_end)
+  --ploidy, "1",
+  -f, $(inputs.ref_fasta)]
+inputs:
+  - id: bam
+    type: File
+  # - id: contig
+  #   type: string
+  # - id: contig_end
+  #   type: int
+  - id: ref_fasta
+    type: File
+outputs:
+  - id: vcf
+    type: stdout
+stdout: var.vcf
-- 
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