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Diffstat (limited to 'workflows/fastq2fasta/bcftools-consensus.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bcftools-consensus.cwl | 24 |
1 files changed, 24 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl new file mode 100644 index 0000000..c111792 --- /dev/null +++ b/workflows/fastq2fasta/bcftools-consensus.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: + - consensus + - -i'QUAL > 1 && GT="A"' + - -Hla + - -f + - $(inputs.ref_fasta) + - $(inputs.vcf) +inputs: + - id: ref_fasta + type: File + - id: vcf + type: File + secondaryFiles: [.csi] +outputs: + - id: out_fasta + type: stdout +stdout: sequence.fasta |