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nucleo.cwl
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class: Workflow
cwlVersion: v1.0
id: nucleo
doc: >-
This workflow takes a READ1 and READ2 fastq.gz file generated for MSK-ACCESS
assay and generated four different Binary Alignment Map file along with
alignment metrics for each.
label: nucleo
$namespaces:
s: 'https://schema.org/'
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: reference_sequence
type: File
doc: >-
Reference sequence file. Please include ".fai", "^.dict", ".amb" , ".sa",
".bwt", ".pac", ".ann" as secondary files if they are not present in the
same location as the ".fasta" file
secondaryFiles:
- .amb
- .fai
- .sa
- ^.dict
- .ann
- .bwt
- .pac
'sbg:x': 0
'sbg:y': 1389.375
- id: gatk_base_recalibrator_known_sites
type:
type: array
items: File
inputBinding:
prefix: '--known-sites'
secondaryFiles:
- .idx
'sbg:x': 0
'sbg:y': 2992.5
- id: sequencing-center
type: string?
'sbg:x': 0
'sbg:y': 1068.75
- id: run-date
type: string?
'sbg:x': 0
'sbg:y': 1282.5
- id: sample
type: string
'sbg:x': 0
'sbg:y': 1175.625
- id: read-structures
type: 'string[]?'
'sbg:x': 0
'sbg:y': 1496.25
- id: read-group-id
type: string
'sbg:x': 0
'sbg:y': 1603.125
- id: platform-unit
type: string
'sbg:x': 0
'sbg:y': 1710
- id: platform-model
type: string?
'sbg:x': 0
'sbg:y': 1816.875
- id: platform
type: string?
'sbg:x': 0
'sbg:y': 1923.75
- id: library
type: string
'sbg:x': 0
'sbg:y': 2351.25
- id: validation_stringency
type: string?
'sbg:x': 0
'sbg:y': 0
- id: UBG_picard_SamToFastq_R1_output_fastq
type: string
'sbg:x': 0
'sbg:y': 213.75
- id: UBG_picard_SamToFastq_R2_output_fastq
type: string
'sbg:x': 0
'sbg:y': 106.875
- id: fastp_read2_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 5343.75
- id: fastp_read2_adapter_sequence
type: string?
'sbg:x': 0
'sbg:y': 5450.625
- id: fastp_read1_output_file_name
type: string
'sbg:x': 0
'sbg:y': 5557.5
- id: fastp_read1_adapter_sequence
type: string?
'sbg:x': 0
'sbg:y': 5664.375
- id: fastp_minimum_read_length
type: int?
'sbg:x': 0
'sbg:y': 5771.25
- id: fastp_html_output_file_name
type: string
'sbg:x': 0
'sbg:y': 6198.75
- id: fastp_json_output_file_name
type: string
'sbg:x': 0
'sbg:y': 6091.875
- id: sort_order
type: string?
'sbg:x': 0
'sbg:y': 961.875
- id: bwa_mem_T
type: int?
'sbg:x': 0
'sbg:y': 6733.125
- id: bwa_mem_Y
type: boolean?
'sbg:x': 0
'sbg:y': 6626.25
- id: UBG_picard_addRG_output_file_name
type: string
'sbg:x': 0
'sbg:y': 427.5
- id: create_bam_index
type: boolean?
'sbg:x': 0
'sbg:y': 6519.375
- id: UBG_bwa_mem_output
type: string
'sbg:x': 0
'sbg:y': 641.25
- id: bwa_mem_K
type: int?
'sbg:x': 0
'sbg:y': 6840
- id: UBG_gatk_merge_bam_alignment_output_file_name
type: string
'sbg:x': 0
'sbg:y': 534.375
- id: optical_duplicate_pixel_distance
type: int?
'sbg:x': 0
'sbg:y': 2137.5
- id: gatk_mark_duplicates_output_file_name
type: string
'sbg:x': 0
'sbg:y': 2565
- id: gatk_mark_duplicates_duplication_metrics_file_name
type: string
'sbg:x': 0
'sbg:y': 2671.875
- id: bedtools_merge_distance_between_features
type: int?
'sbg:x': 0
'sbg:y': 6946.875
- id: bedtools_genomecov_option_bedgraph
type: boolean?
'sbg:x': 0
'sbg:y': 7053.75
- id: apply_bqsr_output_file_name
type: string
'sbg:x': 611.53125
'sbg:y': 4542.1875
- id: abra2_window_size
type: string?
'sbg:x': 0
'sbg:y': 8015.625
- id: abra2_soft_clip_contig
type: string?
'sbg:x': 0
'sbg:y': 8122.5
- id: abra2_scoring_gap_alignments
type: string?
'sbg:x': 0
'sbg:y': 8229.375
- id: UBG_abra2_output_bams
type:
- string
- type: array
items: string
'sbg:x': 0
'sbg:y': 748.125
- id: abra2_no_edge_complex_indel
type: boolean?
'sbg:x': 0
'sbg:y': 8443.125
- id: abra2_maximum_mixmatch_rate
type: float?
'sbg:x': 0
'sbg:y': 8550
- id: abra2_maximum_average_depth
type: int?
'sbg:x': 0
'sbg:y': 8656.875
- id: abra2_consensus_sequence
type: boolean?
'sbg:x': 0
'sbg:y': 8870.625
- id: abra2_bam_index
type: boolean?
'sbg:x': 0
'sbg:y': 8977.5
- id: fgbio_fastq_to_bam_input
type:
type: array
items:
items: File
type: array
'sbg:x': 0
'sbg:y': 4595.625
- id: UBG_picard_fixmateinformation_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 320.625
- id: merge_sam_files_sort_order
type: string?
'sbg:x': 0
'sbg:y': 2244.375
- id: gatk_merge_sam_files_output_file_name
type: string
'sbg:x': 0
'sbg:y': 2458.125
- id: fgbio_collect_duplex_seq_metrics_intervals
type: File?
'sbg:x': 0
'sbg:y': 4809.375
- id: fgbio_group_reads_by_umi_strategy
type: string?
'sbg:x': 0
'sbg:y': 3313.125
- id: fgbio_group_reads_by_umi_output_file_name
type: string
'sbg:x': 0
'sbg:y': 3420
- id: fgbio_group_reads_by_umi_family_size_histogram
type: string
'sbg:x': 0
'sbg:y': 3526.875
- id: fgbio_collect_duplex_seq_metrics_output_prefix
type: string?
'sbg:x': 0
'sbg:y': 4702.5
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
type: boolean?
'sbg:x': 0
'sbg:y': 4916.25
- id: fgbio_call_duplex_consensus_reads_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 5023.125
- id: fgbio_call_duplex_consensus_reads_min_reads
type: 'int[]?'
'sbg:x': 0
'sbg:y': 5130
- id: BC_gatk_sam_to_fastq_output_name_R2
type: string
'sbg:x': 0
'sbg:y': 7374.375
- id: BC_gatk_sam_to_fastq_output_name_R1
type: string
'sbg:x': 0
'sbg:y': 7481.25
- id: BC_picard_fixmate_information_output_file_name
type: string
'sbg:x': 0
'sbg:y': 7160.625
- id: BC_picard_addRG_output_file_name
type: string
'sbg:x': 0
'sbg:y': 7267.5
- id: BC_gatk_merge_bam_alignment_output_file_name
type: string
'sbg:x': 0
'sbg:y': 7588.125
- id: fgbio_postprocessing_output_file_name_simplex
type: string
'sbg:x': 0
'sbg:y': 3206.25
- id: gatk_collect_alignment_summary_metrics_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 2885.625
- id: abra2_contig_anchor
type: string?
'sbg:x': 0
'sbg:y': 8763.75
- id: BC_abra2_output_bams
type:
- string
- type: array
items: string
'sbg:x': 0
'sbg:y': 7801.875
- id: fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex
type: boolean?
'sbg:x': 0
'sbg:y': 3633.75
- id: fgbio_filter_consensus_read_output_file_name_simplex_duplex
type: string
'sbg:x': 0
'sbg:y': 3740.625
- id: fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics
type: string
'sbg:x': 0
'sbg:y': 3847.5
- id: fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics
type: string?
'sbg:x': 0
'sbg:y': 3954.375
- id: fgbio_filter_consensus_read_output_file_name_duplex
type: string?
'sbg:x': 0
'sbg:y': 4061.25
- id: fgbio_filter_consensus_read_min_reads_duplex
type: 'int[]?'
'sbg:x': 0
'sbg:y': 4275
- id: fgbio_filter_consensus_read_min_base_quality_simplex_duplex
type: int?
'sbg:x': 0
'sbg:y': 4381.875
- id: fgbio_filter_consensus_read_min_base_quality_duplex
type: int?
'sbg:x': 0
'sbg:y': 4488.75
- id: BC_bwa_mem_output
type: string
'sbg:x': 0
'sbg:y': 7695
- id: fgbio_filter_consensus_read_min_reads_simplex_duplex
type: 'int[]?'
'sbg:x': 0
'sbg:y': 4168.125
- id: picard_addRG_sort_order
type: string?
'sbg:x': 0
'sbg:y': 2030.625
- id: disable_trim_poly_g
type: boolean?
'sbg:x': 0
'sbg:y': 6305.625
- id: disable_quality_filtering
type: boolean?
'sbg:x': 0
'sbg:y': 6412.5
- id: gatk_base_recalibrator_add_output_sam_program_record
type: boolean?
'sbg:x': 0
'sbg:y': 3099.375
- id: gatk_collect_aln_summary_metrics_bqsr_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 2778.75
- id: abra2_no_sort
type: boolean?
'sbg:x': 0
'sbg:y': 8336.25
- id: base_recalibrator_output_file_name
type: string?
'sbg:x': 0
'sbg:y': 7908.75
- id: temporary_directory
type: string?
'sbg:x': 0
'sbg:y': 855
- id: fgbio_async_io
type: string?
'sbg:x': 0
'sbg:y': 5236.875
- id: fastp_max_len_read2
type: int?
'sbg:x': 0
'sbg:y': 5878.125
- id: fastp_max_len_read1
type: int?
'sbg:x': 0
'sbg:y': 5985
outputs:
- id: fastp_html_output
outputSource:
- uncollapsed_bam_generation/fastp_html_output
type: File
'sbg:x': 1896.48779296875
'sbg:y': 4108.1875
- id: fastp_json_output
outputSource:
- uncollapsed_bam_generation/fastp_json_output
type: File
'sbg:x': 1896.48779296875
'sbg:y': 4001.3125
- id: gatk_collect_alignment_summary_metrics_txt_uncollapsed
outputSource:
- >-
gatk_collect_alignment_summary_metrics_4_1_8_0/gatk_collect_alignment_summary_metrics_txt
type: File
'sbg:x': 3899.757080078125
'sbg:y': 4488.75
- id: indel_realignment_bam
outputSource:
- uncollapsed_bam_generation/indel_realignment_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 1896.48779296875
'sbg:y': 3894.4375
- id: picard_mark_duplicates_metrics
outputSource:
- uncollapsed_bam_generation/picard_mark_duplicates_metrics
type: File
'sbg:x': 1896.48779296875
'sbg:y': 3787.5625
- id: gatk_collect_alignment_summary_metrics_txt_simplex
outputSource:
- bam_collapsing/gatk_collect_alignment_summary_metrics_txt_simplex
type: File
'sbg:x': 3383.319580078125
'sbg:y': 3773.0625
- id: gatk_collect_alignment_summary_metrics_txt_duplex
outputSource:
- bam_collapsing/gatk_collect_alignment_summary_metrics_txt_duplex
type: File
'sbg:x': 3383.319580078125
'sbg:y': 3879.9375
- id: gatk_collect_alignment_summary_metrics_txt_collapsed
outputSource:
- bam_collapsing/gatk_collect_alignment_summary_metrics_txt_collapsed
type: File
'sbg:x': 3383.319580078125
'sbg:y': 3986.8125
- id: fgbio_postprocessing_simplex_bam
outputSource:
- bam_collapsing/fgbio_postprocessing_simplex_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 3383.319580078125
'sbg:y': 4242.5625
- id: fgbio_group_reads_by_umi_histogram
outputSource:
- bam_collapsing/fgbio_group_reads_by_umi_histogram
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4349.4375
- id: fgbio_group_reads_by_umi_bam
outputSource:
- bam_collapsing/fgbio_group_reads_by_umi_bam
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4456.3125
- id: fgbio_filter_consensus_reads_duplex_bam
outputSource:
- bam_collapsing/fgbio_filter_consensus_reads_duplex_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 3383.319580078125
'sbg:y': 4563.1875
- id: fgbio_collect_duplex_seq_metrics_umi_counts
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_umi_counts
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4670.0625
- id: fgbio_collect_duplex_seq_metrics_family_size
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_family_size
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4776.9375
- id: fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4883.8125
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts_txt
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_duplex_umi_counts_txt
type: File
'sbg:x': 3383.319580078125
'sbg:y': 4990.6875
- id: fgbio_collect_duplex_seq_metrics_duplex_qc
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_duplex_qc
type: File
'sbg:x': 3383.319580078125
'sbg:y': 5097.5625
- id: fgbio_collect_duplex_seq_metrics_duplex_family_size
outputSource:
- bam_collapsing/fgbio_collect_duplex_seq_metrics_duplex_family_size
type: File
'sbg:x': 3383.319580078125
'sbg:y': 5204.4375
- id: fgbio_collapsed_bam
outputSource:
- bam_collapsing/fgbio_collapsed_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 3383.319580078125
'sbg:y': 5311.3125
- id: uncollapsed_bam
outputSource:
- base_quality_recalibration/gatk_apply_bqsr_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 3383.319580078125
'sbg:y': 3666.1875
steps:
- id: uncollapsed_bam_generation
in:
- id: sequencing-center
default: MSKCC
source: sequencing-center
- id: sample
source: sample
- id: run-date
source: run-date
- id: read-structures
default:
- 3M2S+T
- 3M2S+T
source:
- read-structures
- id: read-group-id
source: read-group-id
- id: platform-unit
source: platform-unit
- id: platform-model
default: novaseq
source: platform-model
- id: platform
default: ILLUMINA
source: platform
- id: library
source: library
- id: validation_stringency
default: LENIENT
source: validation_stringency
- id: R1_output_fastq
source: UBG_picard_SamToFastq_R1_output_fastq
- id: R2_output_fastq
source: UBG_picard_SamToFastq_R2_output_fastq
- id: reference_sequence
source: reference_sequence
- id: fastp_read2_output_file_name
source: fastp_read2_output_file_name
- id: fastp_read2_adapter_sequence
default: AGATCGGAAGAGC
source: fastp_read2_adapter_sequence
- id: fastp_read1_output_file_name
source: fastp_read1_output_file_name
- id: fastp_read1_adapter_sequence
default: GATCGGAAGAGC
source: fastp_read1_adapter_sequence
- id: fastp_minimum_read_length
default: 25
source: fastp_minimum_read_length
- id: fastp_json_output_file_name
source: fastp_json_output_file_name
- id: fastp_html_output_file_name
source: fastp_html_output_file_name
- id: bwa_mem_Y
default: true
source: bwa_mem_Y
- id: bwa_mem_T
source: bwa_mem_T
- id: sort_order
default: coordinate
source: sort_order
- id: picard_addRG_output_file_name
source: UBG_picard_addRG_output_file_name
- id: bwa_mem_output
source: UBG_bwa_mem_output
- id: bwa_mem_K
source: bwa_mem_K
- id: create_bam_index
default: true
source: create_bam_index
- id: gatk_merge_bam_alignment_output_file_name
source: UBG_gatk_merge_bam_alignment_output_file_name
- id: optical_duplicate_pixel_distance
default: 2500
source: optical_duplicate_pixel_distance
- id: gatk_mark_duplicates_output_file_name
source: gatk_mark_duplicates_output_file_name
- id: gatk_mark_duplicates_duplication_metrics_file_name
source: gatk_mark_duplicates_duplication_metrics_file_name
- id: abra2_window_size
default: '800,700'
source: abra2_window_size
- id: abra2_soft_clip_contig
default: '100,30,80,15'
source: abra2_soft_clip_contig
- id: abra2_scoring_gap_alignments
default: '8,32,48,1'
source: abra2_scoring_gap_alignments
- id: abra2_output_bams
source:
- UBG_abra2_output_bams
- id: abra2_maximum_average_depth
default: 1000
source: abra2_maximum_average_depth
- id: abra2_bam_index
source: abra2_bam_index
- id: abra2_contig_anchor
default: '10,1'
source: abra2_contig_anchor
- id: abra2_consensus_sequence
default: true
source: abra2_consensus_sequence
- id: bedtools_merge_distance_between_features
default: 10
source: bedtools_merge_distance_between_features
- id: abra2_maximum_mixmatch_rate
default: 0.1
source: abra2_maximum_mixmatch_rate
- id: bedtools_genomecov_option_bedgraph
default: true
source: bedtools_genomecov_option_bedgraph
- id: picard_fixmateinformation_output_file_name
source: UBG_picard_fixmateinformation_output_file_name
- id: abra2_no_sort
default: true
source: abra2_no_sort
- id: abra2_no_edge_complex_indel
default: true
source: abra2_no_edge_complex_indel
- id: merge_sam_files_sort_order
default: queryname
source: merge_sam_files_sort_order
- id: gatk_merge_sam_files_output_file_name
source: gatk_merge_sam_files_output_file_name
- id: fgbio_fastq_to_bam_input
source:
- fgbio_fastq_to_bam_input
- id: picard_addRG_sort_order
default: queryname
source: picard_addRG_sort_order
- id: disable_trim_poly_g
default: true
source: disable_trim_poly_g
- id: disable_quality_filtering
default: true
source: disable_quality_filtering
- id: temporary_directory
source: temporary_directory
- id: fgbio_async_io
default: 'true'
source: fgbio_async_io
- id: fastp_max_len_read1
default: 95
source: fastp_max_len_read1
- id: fastp_max_len_read2
default: 95
source: fastp_max_len_read2
out:
- id: gatk_sam_to_fastq_unpaired_fastq
- id: fastp_unpaired2_output
- id: fastp_unpaired1_output
- id: fastp_json_output
- id: fastp_html_output
- id: picard_mark_duplicates_metrics
- id: indel_realignment_bam
run: uncollapsed_bam_generation/uncollapsed_bam_generation.cwl
label: Uncollapsed BAM Generation
'sbg:x': 611.53125
'sbg:y': 4057.3125
- id: bam_collapsing
in:
- id: fgbio_group_reads_by_umi_input
source: uncollapsed_bam_generation/indel_realignment_bam
- id: fgbio_group_reads_by_umi_strategy
default: paired
source: fgbio_group_reads_by_umi_strategy
- id: fgbio_group_reads_by_umi_output_file_name
source: fgbio_group_reads_by_umi_output_file_name
- id: fgbio_group_reads_by_umi_family_size_histogram
source: fgbio_group_reads_by_umi_family_size_histogram
- id: fgbio_collect_duplex_seq_metrics_intervals
source: fgbio_collect_duplex_seq_metrics_intervals
- id: fgbio_collect_duplex_seq_metrics_output_prefix
source: fgbio_collect_duplex_seq_metrics_output_prefix
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
default: true
source: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
- id: fgbio_call_duplex_consensus_reads_read_group_id
source: read-group-id
- id: fgbio_call_duplex_consensus_reads_output_file_name
source: fgbio_call_duplex_consensus_reads_output_file_name
- id: fgbio_call_duplex_consensus_reads_min_reads
default:
- 1
- 1
- 0
source:
- fgbio_call_duplex_consensus_reads_min_reads
- id: reference_sequence
source: reference_sequence
- id: validation_stringency
default: LENIENT
source: validation_stringency
- id: gatk_sam_to_fastq_output_name_R2
source: BC_gatk_sam_to_fastq_output_name_R2
- id: gatk_sam_to_fastq_output_name_R1
source: BC_gatk_sam_to_fastq_output_name_R1
- id: bwa_mem_Y
default: true
source: bwa_mem_Y
- id: bwa_mem_T
source: bwa_mem_T
- id: sort_order
default: coordinate
source: sort_order
- id: picard_addRG_read_group_sequencing_platform
default: ILLUMINA
source: platform
- id: picard_addRG_read_group_sequencing_center
default: MSKCC
source: sequencing-center
- id: picard_addRG_read_group_run_date
source: run-date
- id: picard_addRG_read_group_platform_unit
source: platform-unit
- id: picard_addRG_read_group_library
source: library
- id: picard_addRG_read_group_identifier
source: read-group-id
- id: picard_addRG_output_file_name
source: BC_picard_addRG_output_file_name
- id: bwa_mem_output
source: BC_bwa_mem_output
- id: create_bam_index
default: true
source: create_bam_index
- id: bwa_mem_K
source: bwa_mem_K
- id: abra2_window_size
default: '800,700'
source: abra2_window_size
- id: abra2_soft_clip_contig
default: '100,30,80,15'
source: abra2_soft_clip_contig
- id: abra2_scoring_gap_alignments
default: '8,32,48,1'
source: abra2_scoring_gap_alignments
- id: picard_fixmate_information_output_file_name
source: BC_picard_fixmate_information_output_file_name
- id: abra2_output_bams
source:
- BC_abra2_output_bams
- id: bedtools_genomecov_option_bedgraph
default: true
source: bedtools_genomecov_option_bedgraph
- id: abra2_no_sort
default: true
source: abra2_no_sort
- id: abra2_no_edge_complex_indel
default: true
source: abra2_no_edge_complex_indel
- id: abra2_maximum_mixmatch_rate
default: 0.1
source: abra2_maximum_mixmatch_rate
- id: abra2_maximum_average_depth
default: 1000
source: abra2_maximum_average_depth
- id: bedtools_merge_distance_between_features
default: 10
source: bedtools_merge_distance_between_features
- id: abra2_contig_anchor
default: '10,1'
source: abra2_contig_anchor
- id: abra2_consensus_sequence
default: true
source: abra2_consensus_sequence
- id: gatk_merge_bam_alignment_output_file_name
source: BC_gatk_merge_bam_alignment_output_file_name
- id: fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex
default: true
source: fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex
- id: fgbio_filter_consensus_read_reverse_per_base_tags_duplex
default: true
- id: fgbio_filter_consensus_read_min_base_quality_duplex
default: 30
source: fgbio_filter_consensus_read_min_base_quality_duplex
- id: fgbio_filter_consensus_read_min_base_quality_simplex_duplex
default: 30
source: fgbio_filter_consensus_read_min_base_quality_simplex_duplex
- id: fgbio_filter_consensus_read_min_reads_duplex
default:
- 2
- 1
- 1
source:
- fgbio_filter_consensus_read_min_reads_duplex
- id: fgbio_filter_consensus_read_min_reads_simplex_duplex
default:
- 3
- 3
- 0
source:
- fgbio_filter_consensus_read_min_reads_simplex_duplex
- id: fgbio_filter_consensus_read_output_file_name_simplex_duplex
source: fgbio_filter_consensus_read_output_file_name_simplex_duplex
- id: fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics
source: fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics
- id: fgbio_postprocessing_output_file_name_simplex
source: fgbio_postprocessing_output_file_name_simplex
- id: fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics
source: fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics
- id: fgbio_filter_consensus_read_output_file_name_duplex
source: fgbio_filter_consensus_read_output_file_name_duplex
- id: picard_addRG_read_group_sample_name
source: sample
- id: gatk_collect_alignment_summary_metrics_output_file_name
source: gatk_collect_alignment_summary_metrics_output_file_name
- id: picard_addRG_sort_order
default: queryname
source: picard_addRG_sort_order
- id: temporary_directory
source: temporary_directory
- id: async_io
default: 'true'
source: fgbio_async_io
out:
- id: fgbio_group_reads_by_umi_histogram
- id: fgbio_collect_duplex_seq_metrics_umi_counts
- id: fgbio_collect_duplex_seq_metrics_family_size
- id: fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts_txt
- id: fgbio_collect_duplex_seq_metrics_duplex_qc
- id: fgbio_collect_duplex_seq_metrics_duplex_family_size
- id: gatk_sam_to_fastq_unpaired_fastq
- id: gatk_sam_to_fastq_second_end_fastq
- id: gatk_sam_to_fastq_fastq
- id: gatk_collect_alignment_summary_metrics_txt_simplex
- id: gatk_collect_alignment_summary_metrics_txt_duplex
- id: fgbio_postprocessing_simplex_bam
- id: fgbio_filter_consensus_reads_duplex_bam
- id: fgbio_collapsed_bam
- id: gatk_collect_alignment_summary_metrics_txt_collapsed
- id: fgbio_group_reads_by_umi_bam
- id: fgbio_filter_consensus_reads_simplex_duplex_bam
run: bam_collapsing/bam_collapsing.cwl
label: bam_collapsing
'sbg:x': 1896.48779296875
'sbg:y': 4804.9375
- id: base_quality_recalibration
in:
- id: input
source: uncollapsed_bam_generation/indel_realignment_bam
- id: reference
source: reference_sequence
- id: known_sites
source:
- gatk_base_recalibrator_known_sites
- id: base_recalibrator_output_file_name
source: base_recalibrator_output_file_name
- id: add_output_sam_program_record
default: true
source: gatk_base_recalibrator_add_output_sam_program_record
- id: apply_bqsr_create_output_bam_index
source: create_bam_index
- id: apply_bqsr_output_file_name
source: apply_bqsr_output_file_name
- id: temporary_directory
source: temporary_directory
out:
- id: gatk_apply_bqsr_bam
run: subworkflows/base_quality_recalibration/base_quality_recalibration.cwl
label: base_quality_recalibration
'sbg:x': 1896.48779296875
'sbg:y': 4264.0625
- id: gatk_collect_alignment_summary_metrics_4_1_8_0
in:
- id: input
source: base_quality_recalibration/gatk_apply_bqsr_bam
- id: output_file_name
source: gatk_collect_aln_summary_metrics_bqsr_output_file_name
- id: reference
source: reference_sequence
- id: temporary_directory
source: temporary_directory
out:
- id: gatk_collect_alignment_summary_metrics_txt
run: >-
command_line_tools/gatk_collect_alignment_summary_metrics_4.1.8.0/gatk_collect_alignment_summary_metrics_4.1.8.0.cwl
label: GATK-CollectAlignmentSummaryMetrics
'sbg:x': 3383.319580078125
'sbg:y': 4114.6875
requirements:
- class: SubworkflowFeatureRequirement
$schemas:
- 'http://schema.org/version/latest/schemaorg-current-http.rdf'
's:author':
- class: 's:Person'
's:email': 'mailto:[email protected]'
's:identifier': ''
's:name': Ronak Shah
's:citation': ''
's:codeRepository': 'https://github.com/msk-access/nucleo'
's:contributor':
- class: 's:Person'
's:email': 'mailto:[email protected]'
's:identifier': 'https://orcid.org/0000-0001-9042-6213'
's:name': Ronak Shah
's:dateCreated': '2020-11-23'
's:license': 'https://spdx.org/licenses/Apache-2.0'