/
hybrid_error_correction.cwl
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/
hybrid_error_correction.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
doc: "Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano)"
requirements: {}
inputs:
THREADS:
type: int
INPUT_FASTA:
type: File
INPUT_SHORTREAD:
type: File
steps:
bwa-index:
run: ../../tool/bwa/index/bwa-index.cwl
in:
input_fasta: INPUT_FASTA
out:
- amb
- ann
- bwt
- pac
- sa
bwa-mem:
run: ../../tool/bwa/mem/bwa-mem.cwl
in:
fastq_forward: INPUT_SHORTREAD
index_base: INPUT_FASTA
amb: bwa-index/amb
ann: bwa-index/ann
bwt: bwa-index/bwt
pac: bwa-index/pac
sa: bwa-index/sa
threads: THREADS
out:
- output
samtools-view:
run: ../../tool/samtools/view/samtools-view.cwl
in:
threads: THREADS
input_file: bwa-mem/output
out:
- bam
samtools-sort:
run: ../../tool/samtools/sort/samtools-sort.cwl
in:
input_bamfile: samtools-view/bam
threads: THREADS
out:
- sorted_bam
samtools-index:
run: ../../tool/samtools/index/samtools-index.cwl
in:
input_bamfile: samtools-sort/sorted_bam
out:
- bam_index
pilon:
run: ../../tool/pilon/pilon.cwl
in:
genome_fasta: INPUT_FASTA
aligned_bam: samtools-sort/sorted_bam
bam_index: samtools-index/bam_index
threads: THREADS
out:
- fasta
outputs:
fasta:
type: File
outputSource: pilon/fasta