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allele-vcf-rnaseq-pe.cwl
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allele-vcf-rnaseq-pe.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
inputs:
star_indices_folder:
type: Directory
label: "STAR indices folder for reference genome"
doc: "Path to STAR generated indices for reference genome"
insilico_star_indices_folder:
type: Directory
label: "STAR indices folder for insilico genome"
doc: "Path to STAR generated indices for insilico genome"
chrom_length_file:
type: File
label: "Chromosome length file for reference genome"
format: "http://edamontology.org/format_2330"
doc: "Chromosome length file for reference genome"
strain1:
type: string
label: "I strain name"
doc: "First strain name"
strain2:
type: string
label: "II strain name"
doc: "Second strain name"
strain1_chain_file:
type: File
label: "I strain chain file"
format: "http://edamontology.org/format_2330"
doc: "Chain file to project strain I to reference genome"
strain2_chain_file:
type: File
label: "II strain chain file"
format: "http://edamontology.org/format_2330"
doc: "Chain file to project strain II to reference genome"
threads:
type: int?
default: 2
label: "Number of threads"
doc: "Number of threads for those steps that support multithreading"
fastq_file_upstream:
type: File
label: "FASTQ upstream input file"
format: "http://edamontology.org/format_1930"
doc: "Upstream reads data in a FASTQ format, received after paired end sequencing"
fastq_file_downstream:
type: File
label: "FASTQ downstream input file"
format: "http://edamontology.org/format_1930"
doc: "Downstream reads data in a FASTQ format, received after paired end sequencing"
outputs:
strain1_bigwig:
type: File
format: "http://edamontology.org/format_3006"
label: "I strain bigWig file"
doc: "Generated bigWig file for the first strain"
outputSource: allele_vcf_alignreads_se_pe/strain1_bigwig
strain2_bigwig:
type: File
format: "http://edamontology.org/format_3006"
label: "II strain bigWig file"
doc: "Generated bigWig file for the second strain"
outputSource: allele_vcf_alignreads_se_pe/strain2_bigwig
reference_bigwig:
type: File
format: "http://edamontology.org/format_3006"
label: "Reference bigWig file"
doc: "Generated BigWig file for the reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_bigwig
strain1_bambai_pair:
type: File
format: "http://edamontology.org/format_2572"
label: "Strain I coordinate sorted BAM alignment file (+index BAI)"
doc: "Coordinate sorted BAM file and BAI index file for strain I"
outputSource: allele_vcf_alignreads_se_pe/strain1_bambai_pair
strain2_bambai_pair:
type: File
format: "http://edamontology.org/format_2572"
label: "Strain II coordinate sorted BAM alignment file (+index BAI)"
doc: "Coordinate sorted BAM file and BAI index file for strain II"
outputSource: allele_vcf_alignreads_se_pe/strain2_bambai_pair
reference_bambai_pair:
type: File
format: "http://edamontology.org/format_2572"
label: "Reference coordinate sorted BAM alignment file (+index BAI)"
doc: "Coordinate sorted BAM file and BAI index file for reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_bambai_pair
insilico_star_final_log:
type: File
format: "http://edamontology.org/format_2330"
label: "STAR final log for insilico genome"
doc: "STAR Log.final.out for insilico genome"
outputSource: allele_vcf_alignreads_se_pe/insilico_star_final_log
insilico_star_out_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR log out for insilico genome"
doc: "STAR Log.out for insilico genome"
outputSource: allele_vcf_alignreads_se_pe/insilico_star_out_log
insilico_star_progress_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR progress log for insilico genome"
doc: "STAR Log.progress.out for insilico genome"
outputSource: allele_vcf_alignreads_se_pe/insilico_star_progress_log
insilico_star_stdout_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR stdout log for insilico genome"
doc: "STAR Log.std.out for insilico genome"
outputSource: allele_vcf_alignreads_se_pe/insilico_star_stdout_log
reference_star_final_log:
type: File
format: "http://edamontology.org/format_2330"
label: "STAR final log for reference genome"
doc: "STAR Log.final.out for reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_star_final_log
reference_star_out_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR log out for reference genome"
doc: "STAR Log.out for reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_star_out_log
reference_star_progress_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR progress log for reference genome"
doc: "STAR Log.progress.out for reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_star_progress_log
reference_star_stdout_log:
type: File?
format: "http://edamontology.org/format_2330"
label: "STAR stdout log for reference genome"
doc: "STAR Log.std.out for reference genome"
outputSource: allele_vcf_alignreads_se_pe/reference_star_stdout_log
steps:
extract_fastq_upstream:
run: ../tools/extract-fastq.cwl
in:
compressed_file: fastq_file_upstream
out: [fastq_file]
extract_fastq_downstream:
run: ../tools/extract-fastq.cwl
in:
compressed_file: fastq_file_downstream
out: [fastq_file]
allele_vcf_alignreads_se_pe:
run: ../subworkflows/allele-vcf-alignreads-se-pe.cwl
in:
fastq_files: [extract_fastq_upstream/fastq_file, extract_fastq_downstream/fastq_file]
insilico_star_indices_folder: insilico_star_indices_folder
reference_star_indices_folder: star_indices_folder
reference_chrom_length_file: chrom_length_file
strain1: strain1
strain2: strain2
strain1_chain_file: strain1_chain_file
strain2_chain_file: strain2_chain_file
threads: threads
out:
- strain1_bambai_pair
- strain2_bambai_pair
- reference_bambai_pair
- strain1_bigwig
- strain2_bigwig
- reference_bigwig
- insilico_star_final_log
- insilico_star_out_log
- insilico_star_progress_log
- insilico_star_stdout_log
- reference_star_final_log
- reference_star_out_log
- reference_star_progress_log
- reference_star_stdout_log
$namespaces:
s: http://schema.org/
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
s:name: "allele-vcf-rnaseq-pe"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/allele-vcf-rnaseq-pe.cwl
s:codeRepository: https://github.com/Barski-lab/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:creator:
- class: s:Organization
s:legalName: "Cincinnati Children's Hospital Medical Center"
s:location:
- class: s:PostalAddress
s:addressCountry: "USA"
s:addressLocality: "Cincinnati"
s:addressRegion: "OH"
s:postalCode: "45229"
s:streetAddress: "3333 Burnet Ave"
s:telephone: "+1(513)636-4200"
s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
s:department:
- class: s:Organization
s:legalName: "Allergy and Immunology"
s:department:
- class: s:Organization
s:legalName: "Barski Research Lab"
s:member:
- class: s:Person
s:name: Michael Kotliar
s:email: mailto:misha.kotliar@gmail.com
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
doc: |
Allele specific RNA-Seq (using vcf) paired-end workflow