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# 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
sample_id: string
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
sample_id: sample_id
out: [out_fasta]
run: bcftools-consensus.cwl
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