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workflow_localfiles.cwl
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workflow_localfiles.cwl
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class: Workflow
cwlVersion: v1.0
id: rd_connect
label: RD_Connect
inputs:
- id: fastq_files
type: File[]
- id: reference_genome
type: File[]
- id: known_indels_file
type: File
- id: known_sites_file
type: File
- id: chromosome
type: string
- id: readgroup_str
type: string
- id: sample_name
type: string
outputs:
- id: metrics
outputSource:
- picard_markduplicates/output_metrics
type: File
- id: gvcf
outputSource:
- gatk_haplotype_caller/gvcf
type: File
steps:
- id: unzipped_known_sites
in:
- id: known_sites_file
source:
- known_sites_file
out:
- id: unzipped_known_sites_file
run: gunzip_known_sites.cwl
- id: gunzip
in:
- id: reference_file
source:
- reference_genome
out:
- id: unzipped_fasta
run: gunzip.cwl
- id: picard_dictionary
# from samtools reference genome
in:
- id: reference_genome
source:
- gunzip/unzipped_fasta
# produced .dict file
out:
- id: dict
run: picard_dictionary.cwl
- id: cutadapt2
in:
- id: raw_sequences
source:
- fastq_files
out:
- id: trimmed_fastq
run: cutadapt-v.1.18.cwl
- id: bwa_index
in:
- id: reference_genome
source:
- gunzip/unzipped_fasta
out:
- id: output
run: bwa-index.cwl
- id: samtools_index
in:
- id: input
source:
- gunzip/unzipped_fasta
out:
- id: index_fai
run: samtools_index.cwl
- id: bwa_mem
in:
- id: sample_name
source:
- sample_name
- id: trimmed_fastq
source:
- cutadapt2/trimmed_fastq
- id: read_group
source:
- readgroup_str
- id: reference_genome
source:
- bwa_index/output
out:
- id: aligned_sam
run: bwa-mem.cwl
- id: samtools_sort
in:
- id: input
source:
- bwa_mem/aligned_sam
out:
- id: sorted_bam
run: samtools_sort_bam.cwl
- id: picard_markduplicates
in:
- id: input
source:
- samtools_sort/sorted_bam
out:
- id: md_bam
- id: output_metrics
run: picard_markduplicates.cwl
label: picard-MD
- id: gatk3-rtc
in:
- id: input
source:
- picard_markduplicates/md_bam
- id: reference_genome
source:
- samtools_index/index_fai
- id: dict
source:
- picard_dictionary/dict
- id: known_indels
source:
- known_indels_file
out:
- id: rtc_intervals_file
run: gatk3-rtc.cwl
label: gatk3-rtc
- id: gatk-ir
in:
- id: input
source:
- picard_markduplicates/md_bam
- id: rtc_intervals
source:
- gatk3-rtc/rtc_intervals_file
- id: reference_genome
source:
- samtools_index/index_fai
- id: dict
source:
- picard_dictionary/dict
out:
- id: realigned_bam
run: gatk-ir.cwl
label: gatk-ir
- id: gatk-base_recalibration
in:
- id: reference_genome
source:
- samtools_index/index_fai
- id: dict
source:
- picard_dictionary/dict
- id: input
source:
- gatk-ir/realigned_bam
- id: unzipped_known_sites_file
source:
- unzipped_known_sites/unzipped_known_sites_file
- id: known_indels_file
source:
- known_indels_file
out:
- id: br_model
run: gatk-base_recalibration.cwl
label: gatk-base_recalibration
- id: gatk-base_recalibration_print_reads
in:
- id: reference_genome
source:
- samtools_index/index_fai
- id: dict
source:
- picard_dictionary/dict
- id: input
source:
- gatk-ir/realigned_bam
- id: br_model
source:
- gatk-base_recalibration/br_model
out:
- id: bqsr_bam
run: gatk-base_recalibration_print_reads.cwl
label: gatk-base_recalibration_print_reads
- id: gatk_haplotype_caller
in:
- id: reference_genome
source:
- samtools_index/index_fai
- id: dict
source:
- picard_dictionary/dict
- id: input
source:
- gatk-base_recalibration_print_reads/bqsr_bam
- id: chromosome
source:
- chromosome
out:
- id: gvcf
run: gatk-haplotype_caller.cwl
label: gatk-haplotype_caller
requirements:
- class: MultipleInputFeatureRequirement