/
cram-get-fasta.cwl
71 lines (63 loc) · 1.65 KB
/
cram-get-fasta.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
inputs:
- id: input_cram
type: File
- id: ref_fasta_files
type: File[]
steps:
- id: samtools_seq_cache_populate
run: ../tools/samtools_seq_cache_populate.cwl
in:
ref_fasta_files: ref_fasta_files
out: [ref_cache]
hints:
ResourceRequirement:
ramMin: 100000
coresMin: 1
tmpdirMin: 1000
- id: samtools_fastaref
run: ../tools/samtools/samtools-fastaref.cwl
in:
ref_path_dir: samtools_seq_cache_populate/ref_cache
output_file_name:
default: "reference.fa"
input: input_cram
out: [reference_fasta]
hints:
ResourceRequirement:
ramMin: 8000
coresMin: 1
tmpdirMin: 1000
- id: samtools_faidx
run: ../tools/samtools/samtools-faidx.cwl
in:
fasta: samtools_fastaref/reference_fasta
out: [fasta_index]
- id: samtools_dict
run: ../tools/samtools/samtools-dict.cwl
in:
output:
default: "reference.dict"
fasta: samtools_fastaref/reference_fasta
out: [fasta_dict]
- id: combine_reference_files
in:
main_file: samtools_fastaref/reference_fasta
secondary_files:
- samtools_faidx/fasta_index
- samtools_dict/fasta_dict
out:
[file_with_secondary_files]
run: ../expression-tools/combine_files.cwl
outputs:
- id: reference_fasta
type: File
outputSource: combine_reference_files/file_with_secondary_files
- id: reference_dict
type: File
outputSource: samtools_dict/fasta_dict