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| author | AndreaGuarracino | 2020-09-05 11:51:16 +0200 |
|---|---|---|
| committer | AndreaGuarracino | 2020-09-05 11:51:16 +0200 |
| commit | 556263eae40c2371f85b482494472e165ae4d1d5 (patch) | |
| tree | 4d1c7636f92c115ba441c5a2eaa58435a63d723a /workflows/fastq2fasta | |
| parent | c754aab95f47317228a07ccbe3818780aa22a52a (diff) | |
| download | bh20-seq-resource-556263eae40c2371f85b482494472e165ae4d1d5.tar.gz bh20-seq-resource-556263eae40c2371f85b482494472e165ae4d1d5.tar.lz bh20-seq-resource-556263eae40c2371f85b482494472e165ae4d1d5.zip | |
increased the quality filter threshold
Diffstat (limited to 'workflows/fastq2fasta')
| -rw-r--r-- | workflows/fastq2fasta/bcftools-consensus.cwl | 2 | ||||
| -rw-r--r-- | 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) |