From 556263eae40c2371f85b482494472e165ae4d1d5 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 5 Sep 2020 11:51:16 +0200
Subject: increased the quality filter threshold

---
 workflows/fastq2fasta/bcftools-consensus.cwl | 2 +-
 workflows/fastq2fasta/bcftools-view-qc.cwl   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl
index dffdbe3..4704e79 100644
--- a/workflows/fastq2fasta/bcftools-consensus.cwl
+++ b/workflows/fastq2fasta/bcftools-consensus.cwl
@@ -9,7 +9,7 @@ baseCommand: bcftools
 arguments:
   - consensus
   - -i
-  - 'QUAL > 1 && GT="a"'
+  - 'QUAL > 10 && GT="a"'
   - -Hla
   - -f
   - $(inputs.ref_fasta)
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
index 336f455..37caa19 100644
--- a/workflows/fastq2fasta/bcftools-view-qc.cwl
+++ b/workflows/fastq2fasta/bcftools-view-qc.cwl
@@ -8,7 +8,7 @@ baseCommand: bcftools
 arguments:
   - view
   - -i
-  - 'QUAL > 1 && GT="a"'
+  - 'QUAL > 10 && GT="a"'
   - -Oz
   - --threads=$(inputs.threads)
   - $(inputs.bcf)
-- 
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