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authorAndreaGuarracino2020-09-05 11:51:16 +0200
committerAndreaGuarracino2020-09-05 11:51:16 +0200
commit556263eae40c2371f85b482494472e165ae4d1d5 (patch)
tree4d1c7636f92c115ba441c5a2eaa58435a63d723a /workflows/fastq2fasta
parentc754aab95f47317228a07ccbe3818780aa22a52a (diff)
downloadbh20-seq-resource-556263eae40c2371f85b482494472e165ae4d1d5.tar.gz
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increased the quality filter threshold
Diffstat (limited to 'workflows/fastq2fasta')
-rw-r--r--workflows/fastq2fasta/bcftools-consensus.cwl2
-rw-r--r--workflows/fastq2fasta/bcftools-view-qc.cwl2
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)