diff options
Diffstat (limited to 'workflows/fastq2fasta/bcftools-consensus.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bcftools-consensus.cwl | 9 |
1 files changed, 8 insertions, 1 deletions
diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl index c111792..dffdbe3 100644 --- a/workflows/fastq2fasta/bcftools-consensus.cwl +++ b/workflows/fastq2fasta/bcftools-consensus.cwl @@ -4,20 +4,27 @@ cwlVersion: v1.1 hints: DockerRequirement: dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0" + ShellCommandRequirement: {} baseCommand: bcftools arguments: - consensus - - -i'QUAL > 1 && GT="A"' + - -i + - 'QUAL > 1 && GT="a"' - -Hla - -f - $(inputs.ref_fasta) - $(inputs.vcf) + - {shellQuote: false, valueFrom: "|"} + - sed + - "s/^>.*/>$(inputs.sample_id)/g" inputs: - id: ref_fasta type: File - id: vcf type: File secondaryFiles: [.csi] + - id: sample_id + type: string outputs: - id: out_fasta type: stdout |