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| author | Peter Amstutz | 2020-06-22 18:23:40 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-06-22 18:25:45 +0000 |
| commit | 76883d02e6073f990ea980dad1f8cf21121255ff (patch) | |
| tree | 0fe93dadf69cb5c0c09ff9b98fe18e5baacdd6c4 /workflows/fastq2fasta/bcftools-consensus.cwl | |
| parent | fcf300d0df032f569f21b3ef75a78bb163f55da0 (diff) | |
| download | bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.tar.gz bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.tar.lz bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.zip | |
Adjust QC filter and relabel output sequence with sample_id
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 |