#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
ScatterFeatureRequirement: {}
SchemaDefRequirement:
types:
- $import: ../types/FASTQReadPairType.yml
inputs:
# Intervals should come from capture kit in bed format
intervals: File[]?
interval_padding: int?
# target intervals in picard interval_list format (created from intervals bed file)
target_interval_list: File
# bait intervals in picard interval_list format
bait_interval_list: File
# Read samples, fastq format
# NOTE: GATK best practices recommends unmapped SAM/BAM files
read_pair:
type: ../types/FASTQReadPairType.yml#FASTQReadPairType
# reference genome, fasta
# NOTE: GATK can't handle compressed fasta reference genome
reference_genome:
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
- .fai
- ^.dict
# Number of threads to use for mapping
threads: int
# Read Group annotations
# Can be the project name
library: string
# e.g. Illumina
platform: string
known_sites:
type: File[] # vcf files of known sites, with indexing
secondaryFiles:
- .idx
resource_dbsnp:
type: File
secondaryFiles:
- .idx
outputs:
fastqc_reports:
type: File[]
outputSource: qc/output_qc_report
trim_reports:
type: File[]
outputSource: trim/trim_reports
markduplicates_bam:
type: File
outputSource: mark_duplicates/output_dedup_bam_file
# Recalibration
recalibration_table:
type: File
outputSource: recalibrate_01_analyze/output_recalibration_report
recalibrated_reads:
type: File
outputSource: recalibrate_02_apply_bqsr/output_recalibrated_bam
raw_variants:
type: File
outputSource: variant_calling/output_variants
doc: "VCF file from per sample variant calling"
haplotypes_bam:
type: File
outputSource: variant_calling/output_bam
doc: "BAM file containing assembled haplotypes and locally realigned reads"
steps:
file_pair_details:
run: ../tools/extract-named-file-pair-details.cwl
in:
read_pair: read_pair
library: library
platform: platform
out:
- reads
- read_pair_name
- read_group_header
generate_sample_filenames:
run: ../tools/generate-sample-filenames.cwl
in:
sample_name: file_pair_details/read_pair_name
out:
- combined_reads_output_filenames
- mapped_reads_output_filename
- sorted_reads_output_filename
- dedup_reads_output_filename
- dedup_metrics_output_filename
- recal_reads_output_filename
- recal_table_output_filename
- raw_variants_output_filename
- haplotypes_bam_output_filename
combine_reads:
run: ../tools/concat-gz-files.cwl
requirements:
- class: ResourceRequirement
coresMin: 1
ramMin: 1024
scatter: [files, output_filename]
scatterMethod: dotproduct
in:
files: file_pair_details/reads
output_filename: generate_sample_filenames/combined_reads_output_filenames
out:
- output
qc:
run: ../tools/fastqc.cwl
requirements:
- class: ResourceRequirement
coresMin: 4
ramMin: 3072
scatter: input_fastq_file
in:
input_fastq_file: combine_reads/output
threads:
default: 4
out:
- output_qc_report
trim:
run: ../tools/trim_galore.cwl
requirements:
- class: ResourceRequirement
coresMin: 4
ramMin: 8192
in:
reads: combine_reads/output
paired:
default: true
out:
- trimmed_reads
- trim_reports
map:
run: ../tools/gitc-bwa-mem-samtools.cwl
requirements:
- class: ResourceRequirement
coresMin: $(inputs.threads)
ramMin: 16384
outdirMin: 12288
tmpdirMin: 12288
in:
reads: trim/trimmed_reads
reference: reference_genome
read_group_header: file_pair_details/read_group_header
output_filename: generate_sample_filenames/mapped_reads_output_filename
threads: threads
out:
- output
sort:
run: ../tools/GATK4-SortSam.cwl
requirements:
- class: ResourceRequirement
ramMin: 16384
in:
input_file: map/output
output_sorted_bam_filename: generate_sample_filenames/sorted_reads_output_filename
sort_order: { default: "coordinate" }
java_opt: { default: "-Xms4g" }
out:
- output_sorted_bam
mark_duplicates:
run: ../tools/GATK4-MarkDuplicates.cwl
requirements:
- class: ResourceRequirement
ramMin: 16384
outdirMin: 12288
tmpdirMin: 12288
in:
input_file: sort/output_sorted_bam
output_filename: generate_sample_filenames/dedup_reads_output_filename
metrics_filename: generate_sample_filenames/dedup_metrics_output_filename
validation_stringency: { default: "SILENT" }
assume_sort_order: { default: "coordinate" }
create_index: { default: "true" }
optical_duplicate_pixel_distance: { default: 2500 }
java_opt: { default: "-Xms4g" }
out:
- output_dedup_bam_file
- output_metrics_file
# Now recalibrate
recalibrate_01_analyze:
run: ../tools/GATK4-BaseRecalibrator.cwl
requirements:
- class: ResourceRequirement
ramMin: 8192
in:
reference: reference_genome
input_bam: mark_duplicates/output_dedup_bam_file
output_recalibration_report_filename: generate_sample_filenames/recal_table_output_filename
known_sites: known_sites
intervals: intervals
interval_padding: interval_padding
java_opt: { default: "-Xms4g" }
out:
- output_recalibration_report
recalibrate_02_apply_bqsr:
run: ../tools/GATK4-ApplyBQSR.cwl
requirements:
- class: ResourceRequirement
ramMin: 6144
in:
reference: reference_genome
input_bam: mark_duplicates/output_dedup_bam_file
output_recalibrated_bam_filename: generate_sample_filenames/recal_reads_output_filename
intervals: intervals
interval_padding: interval_padding
bqsr_report: recalibrate_01_analyze/output_recalibration_report
add_output_sam_program_record: { default: true }
java_opt: { default: "-Xms3g" }
out:
- output_recalibrated_bam
variant_calling:
run: ../tools/GATK4-HaplotypeCaller.cwl
requirements:
- class: ResourceRequirement
coresMin: 1
ramMin: 14336
in:
reference: reference_genome
input_bam: recalibrate_02_apply_bqsr/output_recalibrated_bam
# Naming your output file using the .g.vcf extension will automatically set the appropriate values for --variant_index_type and --variant_index_parameter
output_variants_filename: generate_sample_filenames/raw_variants_output_filename
output_bam_filename: generate_sample_filenames/haplotypes_bam_output_filename
intervals: intervals
interval_padding: interval_padding
annotation_groups: { default: ['StandardAnnotation','AS_StandardAnnotation'] }
emit_ref_confidence: { default: "GVCF" }
java_opt: { default: "-Xms7g" }
out:
- output_variants
- output_bam