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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/fastq2fasta-create-bwaindex.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/fastq2fasta-create-bwaindex.cwl')
| -rw-r--r-- | workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl new file mode 100644 index 0000000..dab7ff2 --- /dev/null +++ b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl @@ -0,0 +1,41 @@ +cwlVersion: v1.1 +class: Workflow +requirements: + SubworkflowFeatureRequirement: {} +hints: + ResourceRequirement: + ramMin: 3000 + +inputs: + ref_fasta: + type: File + fastq_forward: + type: File + fastq_reverse: + type: File? + threads: + type: int + default: 4 + +outputs: + out_fasta: + type: File + outputSource: fastq2fasta/out_fasta + +steps: + bwa-index: + in: {input_fasta: ref_fasta} + out: [indexed_fasta] + run: bwa-index.cwl + samtools-faidx: + in: {input_fasta: bwa-index/indexed_fasta} + out: [indexed_fasta] + run: samtools-faidx.cwl + fastq2fasta: + in: + fastq_forward: fastq_forward + fastq_reverse: fastq_reverse + ref_fasta: samtools-faidx/indexed_fasta + threads: threads + out: [out_fasta] + run: fastq2fasta.cwl |