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Diffstat (limited to 'workflows/fastq2fasta/freebayes.cwl')
| -rw-r--r-- | workflows/fastq2fasta/freebayes.cwl | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/freebayes.cwl b/workflows/fastq2fasta/freebayes.cwl new file mode 100644 index 0000000..1bf9b2f --- /dev/null +++ b/workflows/fastq2fasta/freebayes.cwl @@ -0,0 +1,25 @@ +#!/usr/bin/env cwl-runner +class: CommandLineTool +cwlVersion: v1.1 +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/freebayes:1.3.2--py37hc088bd4_0" +baseCommand: freebayes +arguments: [ + --bam, $(inputs.bam), + # --region=$(inputs.contig):1-$(inputs.contig_end) + --ploidy, "1", + -f, $(inputs.ref_fasta)] +inputs: + - id: bam + type: File + # - id: contig + # type: string + # - id: contig_end + # type: int + - id: ref_fasta + type: File +outputs: + - id: vcf + type: stdout +stdout: var.vcf |