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authorPeter Amstutz2020-04-20 12:55:18 -0400
committerPeter Amstutz2020-04-20 12:55:18 -0400
commitd781e42c9adac07253cb928ae66e9b7314710267 (patch)
tree4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/fastq2fasta/bcftools-view-qc.cwl
parent1219eaf496c899f3043b90e30eb956f0f363bfb3 (diff)
downloadbh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.gz
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Move workflows into main repo
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/fastq2fasta/bcftools-view-qc.cwl')
-rw-r--r--workflows/fastq2fasta/bcftools-view-qc.cwl24
1 files changed, 24 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
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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