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rnaseq_pipeline_fastq_checker.cwl
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rnaseq_pipeline_fastq_checker.cwl
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#!/usr/bin/env cwl-runner
doc: |
A workflow to verify the proper execution of [TOPMed RNA-seq Workflow](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl)
cwlVersion: v1.0
class: Workflow
id: "RNAseq-checker"
label: "RNAseq-checker"
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: SubworkflowFeatureRequirement
inputs:
star_index:
type: Directory
fastqs:
type: File[]
prefix_str:
type: string
rsem_ref_dir:
type: Directory
max_frag_len:
type: int
estimate_rspd:
type: boolean
is_stranded:
type: boolean
paired_end:
type: boolean
genes_gtf:
type: File
genome_fasta:
type: File
secondaryFiles:
- .fai
- ^.dict
rnaseqc_flags:
type: string[]
# gatk_flags:
# type:
# type: "null"
# type: array
# items: string
hash_count_metrics:
type: string
hash_chimeric_junctions:
type: string
hash_read_counts:
type: string
hash_junctions:
type: string
hash_junctions_pass1:
type: string
# hash_markduplicates_metrics:
# type: string
hash_gene_results:
type: string
hash_isoforms_results:
type: string
# hash_gene_rpkm:
# type: string
# hash_gene_counts:
# type: string
# hash_exon_counts:
# type: string
# hash_count_outputs:
# type: string
checker_star_output_bam:
type: File
checker_transcriptome_bam:
type: File
checker_chimeric_bam_file:
type: File
checker_markduplicates_bam:
type: File
known_str:
type: string
outputs:
check_star_output_bam_str:
type: string
outputSource: check_star_output_bam/out_string
check_transcriptome_bam_str:
type: string
outputSource: check_transcriptome_bam/out_string
check_chimeric_bam_str:
type: string
outputSource: check_chimeric_bam/out_string
check_markduplicates_bam_str:
type: string
outputSource: check_markduplicates_bam/out_string
check_chimeric_junctions_hash:
type: string
outputSource: check_chimeric_junctions/out_hash_string
check_read_counts_hash:
type: string
outputSource: check_read_counts/out_hash_string
check_junctions_hash:
type: string
outputSource: check_junctions/out_hash_string
check_junctions_pass1_hash:
type: string
outputSource: check_junctions_pass1/out_hash_string
# check_markduplicates_metrics_hash:
# type: string
# outputSource: check_markduplicates_metrics/out_hash_string
check_gene_results_hash:
type: string
outputSource: check_gene_results/out_hash_string
check_isoforms_results_hash:
type: string
outputSource: check_isoforms_results/out_hash_string
# check_gene_rpkm_hash:
# type: string
# outputSource: check_gene_rpkm/out_hash_string
# check_gene_counts_hash:
# type: string
# outputSource: check_gene_counts/out_hash_string
# check_exon_counts_hash:
# type: string
# outputSource: check_exon_counts/out_hash_string
check_count_metrics_hash:
type: string
outputSource: check_count_metrics/out_hash_string
# check_count_outputs_hash:
# type: string
# outputSource: check_count_outputs/out_hash_string
steps:
run_rnaseq_pipeline:
run: ../rnaseq_pipeline_fastq.cwl
in:
star_index: star_index
fastqs: fastqs
prefix_str: prefix_str
rsem_ref_dir: rsem_ref_dir
max_frag_len: max_frag_len
estimate_rspd: estimate_rspd
is_stranded: is_stranded
paired_end: paired_end
genes_gtf: genes_gtf
genome_fasta: genome_fasta
rnaseqc_flags: rnaseqc_flags
# gatk_flags: gatk_flags
out:
[
star_output_bam,
star_output_bam_index,
star_output_transcriptome_bam,
star_output_chimeric_junctions,
star_output_chimeric_bam_file,
star_output_chimeric_bam_index,
star_output_read_counts,
star_output_junctions,
star_output_junctions_pass1,
star_output_logs,
markduplicates_output_bam,
markduplicates_output_metrics,
markduplicates_bam_index,
rsem_output_gene_results,
rsem_output_isoforms_results,
rna-seqc_output_gene_rpkm,
rna-seqc_output_gene_counts,
rna-seqc_output_exon_counts,
rna-seqc_output_count_metrics,
rna-seqc_output_count_outputs
]
check_star_output_bam:
run: check_bams_wf.cwl
in:
bam_one: run_rnaseq_pipeline/star_output_bam
bam_two: checker_star_output_bam
known_str: known_str
out: [out_string]
check_transcriptome_bam:
run: check_bams_wf.cwl
in:
bam_one: run_rnaseq_pipeline/star_output_transcriptome_bam
bam_two: checker_transcriptome_bam
known_str: known_str
out: [out_string]
check_chimeric_bam:
run: check_bams_wf.cwl
in:
bam_one: run_rnaseq_pipeline/star_output_chimeric_bam_file
bam_two: checker_chimeric_bam_file
known_str: known_str
out: [out_string]
check_markduplicates_bam:
run: check_bams_wf.cwl
in:
bam_one: run_rnaseq_pipeline/markduplicates_output_bam
bam_two: checker_markduplicates_bam
known_str: known_str
out: [out_string]
check_chimeric_junctions:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/star_output_chimeric_junctions
input_hash: hash_chimeric_junctions
out: [out_hash_string]
check_read_counts:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/star_output_read_counts
input_hash: hash_read_counts
out: [out_hash_string]
check_junctions:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/star_output_junctions
input_hash: hash_junctions
out: [out_hash_string]
check_junctions_pass1:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/star_output_junctions_pass1
input_hash: hash_junctions_pass1
out: [out_hash_string]
# check_markduplicates_metrics:
# run: check_md5_wf.cwl
# in:
# file_to_check: run_rnaseq_pipeline/markduplicates_output_metrics
# input_hash: hash_markduplicates_metrics
# out: [out_hash_string]
check_gene_results:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/rsem_output_gene_results
input_hash: hash_gene_results
out: [out_hash_string]
check_isoforms_results:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/rsem_output_isoforms_results
input_hash: hash_isoforms_results
out: [out_hash_string]
# check_gene_rpkm:
# run: check_md5_wf.cwl
# in:
# file_to_check: run_rnaseq_pipeline/rna-seqc_output_gene_rpkm
# input_hash: hash_gene_rpkm
# out: [out_hash_string]
# check_gene_counts:
# run: check_md5_wf.cwl
# in:
# file_to_check: run_rnaseq_pipeline/rna-seqc_output_gene_counts
# input_hash: hash_gene_counts
# out: [out_hash_string]
# check_exon_counts:
# run: check_md5_wf.cwl
# in:
# file_to_check: run_rnaseq_pipeline/rna-seqc_output_exon_counts
# input_hash: hash_exon_counts
# out: [out_hash_string]
check_count_metrics:
run: check_md5_wf.cwl
in:
file_to_check: run_rnaseq_pipeline/rna-seqc_output_count_metrics
input_hash: hash_count_metrics
out: [out_hash_string]
# check_count_outputs:
# run: check_md5_wf.cwl
# in:
# file_to_check: run_rnaseq_pipeline/rna-seqc_output_count_outputs
# input_hash: hash_count_outputs
# out: [out_hash_string]
$namespaces:
s: http://schema.org/
$schemas:
- http://dublincore.org/2012/06/14/dcterms.rdf
- http://xmlns.com/foaf/spec/20140114.rdf
- https://schema.org/docs/schema_org_rdfa.html
s:author:
- class: s:Person
s:id: https://orcid.org/0000-0003-3523-5312
s:email: christopherball@rti.org
s:name: Christopher Ball
s:codeRepository: https://github.com/heliumdatacommons/cwl_workflows