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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/bam2fasta.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/bam2fasta.cwl')
| -rw-r--r-- | workflows/fastq2fasta/bam2fasta.cwl | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bam2fasta.cwl b/workflows/fastq2fasta/bam2fasta.cwl new file mode 100644 index 0000000..efe580f --- /dev/null +++ b/workflows/fastq2fasta/bam2fasta.cwl @@ -0,0 +1,65 @@ +# Reference: +# https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/freebayes.sh +# https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/consensus.sh +class: Workflow +cwlVersion: v1.1 +id: bam2fasta +label: bam2fasta +requirements: [] + +inputs: + bam: + type: File + fasta: + type: File + threads: + type: int + default: 4 + +outputs: + out_fasta: + type: File + outputSource: bcftools_consensus/out_fasta + +steps: + freebayes: + in: + bam: bam + ref_fasta: fasta + out: [vcf] + run: freebayes.cwl + bcftools_view_exclude_ref: + in: + vcf: freebayes/vcf + threads: threads + out: [bcf] + run: bcftools-view-exclude-ref.cwl + bcftools_norm: + in: + ref_fasta: fasta + bcf: bcftools_view_exclude_ref/bcf + threads: threads + out: [normalized_bcf] + run: bcftools-norm.cwl + bcftools_index_after_normalization: + in: + bcf: bcftools_norm/normalized_bcf + out: [indexed] + run: bcftools-index.cwl + bcftools_view_qc: + in: + bcf: bcftools_index_after_normalization/indexed + threads: threads + out: [vcf] + run: bcftools-view-qc.cwl + bcftools_index_after_qc: + in: + bcf: bcftools_view_qc/vcf + out: [indexed] + run: bcftools-index.cwl + bcftools_consensus: + in: + ref_fasta: fasta + vcf: bcftools_index_after_qc/indexed + out: [out_fasta] + run: bcftools-consensus.cwl |