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| author | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 12:55:18 -0400 |
| commit | d781e42c9adac07253cb928ae66e9b7314710267 (patch) | |
| tree | 4718165cbc069169eaff98080c61c5f07763ffc1 /workflows/fastq2fasta/freebayes.cwl | |
| parent | 1219eaf496c899f3043b90e30eb956f0f363bfb3 (diff) | |
| download | bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.gz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.tar.lz bh20-seq-resource-d781e42c9adac07253cb928ae66e9b7314710267.zip | |
Move workflows into main repo
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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 |