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Diffstat (limited to 'workflows/fastq2fasta/bcftools-view-exclude-ref.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bcftools-view-exclude-ref.cwl | 23 |
1 files changed, 23 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl b/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl new file mode 100644 index 0000000..849bd88 --- /dev/null +++ b/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl @@ -0,0 +1,23 @@ +#!/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 + - --no-version + - -Ou + - -e'type=ref' + - --threads=$(inputs.threads) + - $(inputs.vcf) +inputs: + - id: vcf + type: File + - id: threads + type: int +outputs: + - id: bcf + type: stdout +stdout: $(inputs.vcf.nameroot).without-ref.bcf |