From 76883d02e6073f990ea980dad1f8cf21121255ff Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 22 Jun 2020 18:23:40 +0000
Subject: Adjust QC filter and relabel output sequence with sample_id

---
 workflows/fastq2fasta/bcftools-view-qc.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
index 477c596..336f455 100644
--- a/workflows/fastq2fasta/bcftools-view-qc.cwl
+++ b/workflows/fastq2fasta/bcftools-view-qc.cwl
@@ -8,7 +8,7 @@ baseCommand: bcftools
 arguments:
   - view
   - -i
-  - 'QUAL>1 && (GT="AA" || GT="Aa")'
+  - 'QUAL > 1 && GT="a"'
   - -Oz
   - --threads=$(inputs.threads)
   - $(inputs.bcf)
-- 
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