1 files changed, 24 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
new file mode 100644
index 0000000..477c596
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-view-qc.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:
+  - view
+  - -i
+  - 'QUAL>1 && (GT="AA" || GT="Aa")'
+  - -Oz
+  - --threads=$(inputs.threads)
+  - $(inputs.bcf)
+inputs:
+  - id: threads
+    type: int
+  - id: bcf
+    type: File
+    secondaryFiles: [.csi]
+outputs:
+  - id: vcf
+    type: stdout
+stdout: out.changes.vcf.gz