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Diffstat (limited to 'workflows/fastq2fasta/bwa-index.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bwa-index.cwl | 32 |
1 files changed, 32 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bwa-index.cwl b/workflows/fastq2fasta/bwa-index.cwl new file mode 100644 index 0000000..775ba8d --- /dev/null +++ b/workflows/fastq2fasta/bwa-index.cwl @@ -0,0 +1,32 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.1 +class: CommandLineTool +doc: string +requirements: + DockerRequirement: + dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5 + InitialWorkDirRequirement: + listing: + - $(inputs.input_fasta) +baseCommand: [bwa, index] +inputs: + input_fasta: + type: File + label: "input fasta file" + inputBinding: + position: 1 +outputs: + indexed_fasta: + type: File + outputBinding: + glob: $(inputs.input_fasta.basename) + secondaryFiles: + - .amb + - .ann + - .bwt + - .pac + - .sa + stdout: stdout + stderr: stderr +stdout: bwa-index-stdout.log +stderr: bwa-index-stderr.log |