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-consensus.cwl | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 workflows/fastq2fasta/bcftools-consensus.cwl

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

diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl
new file mode 100644
index 0000000..c111792
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-consensus.cwl
@@ -0,0 +1,24 @@
+#!/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:
+  - consensus
+  - -i'QUAL > 1 && GT="A"'
+  - -Hla
+  - -f
+  - $(inputs.ref_fasta)
+  - $(inputs.vcf)
+inputs:
+  - id: ref_fasta
+    type: File
+  - id: vcf
+    type: File
+    secondaryFiles: [.csi]
+outputs:
+  - id: out_fasta
+    type: stdout
+stdout: sequence.fasta
-- 
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