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bam_collapsing.cwl
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class: Workflow
cwlVersion: v1.0
id: bam_collapsing
doc: >-
This is the workflow is written using Common Workflow Language (CWL) version
1.0 (https://www.commonwl.org/v1.0/) and is used at Memorial Sloan Kettering
Cancer Center for producing collapsed bam files from data generated for the NY
state-approved MSK-ACCESS assay.
label: bam_collapsing
$namespaces:
s: 'https://schema.org/'
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: fgbio_group_reads_by_umi_input
type: File
doc: 'Fgbio GroupReadsByUmi: The input BAM file.'
secondaryFiles:
- ^.bai
'sbg:x': 0
'sbg:y': 2774.9375
- id: fgbio_group_reads_by_umi_strategy
type: string
doc: >-
Fgbio GroupReadsByUmi: The UMI assignment strategy.(identity, edit,
adjacency, paired)
'sbg:x': 0
'sbg:y': 2348
- id: fgbio_group_reads_by_umi_raw_tag
type: string?
doc: 'Fgbio GroupReadsByUmi: The tag containing the raw UMI. (Default:RX)'
'sbg:x': 0
'sbg:y': 2454.734375
- id: fgbio_group_reads_by_umi_output_file_name
type: string?
doc: 'Fgbio GroupReadsByUmi: The output BAM file name'
'sbg:x': 0
'sbg:y': 2561.46875
- id: fgbio_group_reads_by_umi_min_umi_length
type: int?
doc: >-
Fgbio GroupReadsByUmi: The minimum UMI length. If not specified then all
UMIs must have the same length, otherwise discard reads with UMIs shorter
than this length and allow for differing UMI lengths.
'sbg:x': 0
'sbg:y': 2668.203125
- id: fgbio_group_reads_by_umi_include_non_pf_reads
type: boolean?
doc: 'Fgbio GroupReadsByUmi: Include non-PF reads.'
'sbg:x': 0
'sbg:y': 2881.671875
- id: fgbio_group_reads_by_umi_family_size_histogram
type: string
doc: 'Fgbio GroupReadsByUmi: Optional output of tag family size counts.'
'sbg:x': 0
'sbg:y': 2988.40625
- id: fgbio_group_reads_by_umi_edits
type: int?
doc: 'Fgbio GroupReadsByUmi: The allowable number of edits between UMIs.'
'sbg:x': 0
'sbg:y': 3095.140625
- id: fgbio_group_reads_by_umi_assign_tag
type: string?
doc: 'Fgbio GroupReadsByUmi: The output tag for UMI grouping. (Default:MI)'
'sbg:x': 0
'sbg:y': 3201.875
- id: fgbio_collect_duplex_seq_metrics_intervals
type: File?
doc: >-
Fgbio CollectDuplexSeqMetrics: Optional set of intervals over which to
restrict analysis.
'sbg:x': 0
'sbg:y': 3735.546875
- id: fgbio_collect_duplex_seq_metrics_output_prefix
type: string?
doc: 'Fgbio CollectDuplexSeqMetrics: Prefix of output files to write.'
'sbg:x': 0
'sbg:y': 3308.609375
- id: fgbio_collect_duplex_seq_metrics_min_ba_reads
type: int?
doc: >-
Fgbio CollectDuplexSeqMetrics: Minimum BA reads to call a tag family a
‘duplex’.
'sbg:x': 0
'sbg:y': 3415.34375
- id: fgbio_collect_duplex_seq_metrics_min_ab_reads
type: int?
doc: >-
Fgbio CollectDuplexSeqMetrics: Minimum AB reads to call a tag family a
‘duplex’.
'sbg:x': 0
'sbg:y': 3522.078125
- id: fgbio_collect_duplex_seq_metrics_mi_tag
type: string?
doc: >-
Fgbio CollectDuplexSeqMetrics: The output tag for UMI grouping. (Default:
MI)
'sbg:x': 0
'sbg:y': 3628.8125
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
type: boolean
doc: >-
Fgbio CollectDuplexSeqMetrics: If true, produce the .duplex_umi_counts.txt
file with counts of duplex UMI observations.
'sbg:x': 0
'sbg:y': 3842.28125
- id: fgbio_collect_duplex_seq_metrics_description
type: string?
doc: >-
Fgbio CollectDuplexSeqMetrics:Description of data set used to label plots.
Defaults to sample/library.
'sbg:x': 0
'sbg:y': 3949.015625
- id: fgbio_call_duplex_consensus_reads_trim
type: boolean?
doc: >-
Fgbio CallDuplexConsensusReads : If true, quality trim input reads in
addition to masking low Q bases.
'sbg:x': 0
'sbg:y': 4055.75
- id: fgbio_call_duplex_consensus_reads_sort_order
type: string?
doc: >-
Fgbio CallDuplexConsensusReads: The sort order of the output, if :none:
then the same as the input.
'sbg:x': 0
'sbg:y': 4162.484375
- id: fgbio_call_duplex_consensus_reads_read_name_prefix
type: string?
doc: 'Fgbio CallDuplexConsensusReads: The prefix all consensus read names'
'sbg:x': 0
'sbg:y': 4269.21875
- id: fgbio_call_duplex_consensus_reads_read_group_id
type: string?
doc: >-
Fgbio CallDuplexConsensusReads: The new read group ID for all the
consensus reads.
'sbg:x': 0
'sbg:y': 4375.953125
- id: fgbio_call_duplex_consensus_reads_output_file_name
type: string?
doc: >-
Fgbio CallDuplexConsensusReads: Output SAM or BAM file to write consensus
reads.
'sbg:x': 0
'sbg:y': 4482.6875
- id: fgbio_call_duplex_consensus_reads_min_reads
type: 'int[]'
doc: >-
Fgbio CallDuplexConsensusReads: The minimum number of input reads to a
consensus read.
'sbg:x': 0
'sbg:y': 4589.421875
- id: fgbio_call_duplex_consensus_reads_min_input_base_quality
type: int?
doc: >-
Fgbio CallDuplexConsensusReads: Ignore bases in raw reads that have Q
below this value.
'sbg:x': 0
'sbg:y': 4696.15625
- id: fgbio_call_duplex_consensus_reads_max_reads_per_strand
type: int?
doc: >-
Fgbio CallDuplexConsensusReads: The maximum number of reads to use when
building a single-strand consensus. If more than this many reads are
present in a tag family, the family is randomly downsampled to exactly
max-reads reads.
'sbg:x': 0
'sbg:y': 4802.890625
- id: fgbio_call_duplex_consensus_reads_error_rate_pre_umi
type: int?
doc: >-
Fgbio CallDuplexConsensusReads: The Phred-scaled error rate for an error
prior to the UMIs being integrated.
'sbg:x': 0
'sbg:y': 4909.625
- id: fgbio_call_duplex_consensus_reads_error_rate_post_umi
type: int?
doc: >-
Fgbio CallDuplexConsensusReads: The Phred-scaled error rate for an error
post the UMIs have been integrated.
'sbg:x': 0
'sbg:y': 5016.359375
- id: reference_sequence
type: File
doc: >-
Reference sequence file. Please include ".fai", "^.dict", ".amb" , ".sa",
".bwt", ".pac" as secondary files if they are not present in the same
location as the ".fasta" file
secondaryFiles:
- .fai
- ^.dict
- .amb
- .sa
- .ann
- .bwt
- .pac
'sbg:x': 0
'sbg:y': 320.15625
- id: validation_stringency
type: string
doc: >-
GATK Validation stringency for all SAM files read by this program. Setting
stringency to SILENT can improve performance when processing a BAM file in
which variable-length data (read, qualities, tags) do not otherwise need
to be decoded.
'sbg:x': 0
'sbg:y': 0
- id: gatk_sam_to_fastq_output_name_unpaired
type: string?
doc: 'GATK SamToFastq: unpaired fastq output file name'
'sbg:x': 0
'sbg:y': 1600.859375
- id: gatk_sam_to_fastq_output_name_R2
type: string
doc: 'GATK SamToFastq: R2 fastq.gz output file name'
'sbg:x': 0
'sbg:y': 1707.59375
- id: gatk_sam_to_fastq_include_non_primary_alignments
type: boolean?
doc: >-
GATK SamToFastq: If true, include non-primary alignments in the output.
Support of non-primary alignments in SamToFastq is not comprehensive, so
there may be exceptions if this is set to true and there are paired reads
with non-primary alignments.
'sbg:x': 0
'sbg:y': 1921.0625
- id: gatk_sam_to_fastq_include_non_pf_reads
type: boolean?
doc: >-
GATK SamToFastq: Include non-PF reads from the SAM file into the output
FASTQ files. PF means 'passes filtering'. Reads whose 'not passing quality
controls' flag is set are non-PF reads. See GATK Dictionary for more info.
'sbg:x': 0
'sbg:y': 2027.796875
- id: gatk_sam_to_fastq_output_name_R1
type: string
doc: 'GATK SamToFastq: R1 fastq.gz output file name'
'sbg:x': 0
'sbg:y': 1814.328125
- id: bwa_mem_Y
type: boolean?
doc: >-
bwa mem: to force soft-clipping rather than default hard-clipping of
supplementary alignments
'sbg:x': 0
'sbg:y': 5229.78125
- id: bwa_mem_T
type: int?
doc: >-
bwa mem: Don’t output alignment with score lower than INT. This option
only affects output.
'sbg:x': 0
'sbg:y': 5336.484375
- id: sort_order
type: string
doc: The order in which the merged reads should be output.
'sbg:x': 0
'sbg:y': 213.453125
- id: picard_addRG_read_group_sequencing_platform
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group platform (e.g. ILLUMINA, SOLID)'
'sbg:x': 0
'sbg:y': 640.28125
- id: picard_addRG_read_group_sequencing_center
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group sequencing center name'
'sbg:x': 0
'sbg:y': 747.015625
- id: picard_addRG_read_group_run_date
type: string?
doc: 'PicardAddOrReplaceReadGroups: Read-Group Run date'
'sbg:x': 0
'sbg:y': 960.484375
- id: picard_addRG_read_group_platform_unit
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group Platform Unit (eg. run barcode)'
'sbg:x': 0
'sbg:y': 1067.21875
- id: picard_addRG_read_group_library
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group library'
'sbg:x': 0
'sbg:y': 1173.953125
- id: picard_addRG_read_group_identifier
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group ID'
'sbg:x': 0
'sbg:y': 1280.6875
- id: picard_addRG_read_group_description
type: string?
doc: 'PicardAddOrReplaceReadGroups: Read-Group Description'
'sbg:x': 0
'sbg:y': 1387.421875
- id: picard_addRG_output_file_name
type: string?
doc: PicardAddOrReplaceReadGroups output file name
'sbg:x': 0
'sbg:y': 1494.140625
- id: bwa_mem_P
type: boolean?
doc: >-
bwa mem : In the paired-end mode, perform SW to rescue missing hits only
but do not try to find hits that fit a proper pair.
'sbg:x': 0
'sbg:y': 5443.1875
- id: bwa_mem_output
type: string?
doc: 'bwa mem: Output SAM file name'
'sbg:x': 0
'sbg:y': 5549.890625
- id: create_bam_index
type: boolean?
'sbg:x': 2248.361328125
'sbg:y': 2901.7421875
- id: bwa_mem_M
type: boolean?
doc: Mark shorter split hits as secondary
'sbg:x': 0
'sbg:y': 5656.59375
- id: bwa_mem_K
type: int?
doc: >-
bwa mem : to achieve deterministic alignment results (Note: this is a
hidden option)
'sbg:x': 0
'sbg:y': 5763.296875
- id: abra2_window_size
type: string?
doc: 'Processing window size and overlap (size,overlap) (default: 400,200)'
'sbg:x': 3001.30419921875
'sbg:y': 2614.8671875
- id: abra2_soft_clip_contig
type: string?
doc: >-
Soft clip contig args
[max_contigs,min_base_qual,frac_high_qual_bases,min_soft_clip_len]
(default:16,13,80,15)
'sbg:x': 3001.30419921875
'sbg:y': 2721.5859375
- id: abra2_scoring_gap_alignments
type: string?
doc: >-
Scoring used for contig alignments(match,
mismatch_penalty,gap_open_penalty,gap_extend_penalty) (default:8,32,48,1)
'sbg:x': 3001.30419921875
'sbg:y': 2828.3203125
- id: picard_fixmate_information_output_file_name
type: string?
doc: 'PicardFixMateInformaiton: The output file to write to'
'sbg:x': 0
'sbg:y': 426.859375
- id: abra2_output_bams
type:
- string
- type: array
items: string
doc: Required list of output sam or bam file (s) separated by comma
'sbg:x': 3001.30419921875
'sbg:y': 2935.0390625
- id: bedtools_genomecov_option_bedgraph
type: boolean?
doc: >-
option flag parameter to choose output file format. -bg refers to bedgraph
format
'sbg:x': 3001.30419921875
'sbg:y': 2508.1484375
- id: abra2_no_sort
type: boolean?
doc: Do not attempt to sort final output
'sbg:x': 3001.30419921875
'sbg:y': 3041.7421875
- id: abra2_no_edge_complex_indel
type: boolean?
doc: Prevent output of complex indels at read start or read end
'sbg:x': 3001.30419921875
'sbg:y': 3148.4609375
- id: abra2_maximum_mixmatch_rate
type: float?
doc: >-
Max allowed mismatch rate when mapping reads back to contigs (default:
0.05)
'sbg:x': 3001.30419921875
'sbg:y': 3255.1796875
- id: abra2_maximum_average_depth
type: int?
doc: >-
Regions with average depth exceeding this value will be downsampled
(default: 1000)
'sbg:x': 3001.30419921875
'sbg:y': 3361.8984375
- id: bedtools_merge_distance_between_features
type: int?
doc: Maximum distance between features allowed for features to be merged.
'sbg:x': 3001.30419921875
'sbg:y': 2401.4140625
- id: abra2_contig_anchor
type: string?
doc: >-
Contig anchor [M_bases_at_contig_edge,max_mismatches_near_edge]
(default:10,2)
'sbg:x': 3001.30419921875
'sbg:y': 3468.6328125
- id: abra2_consensus_sequence
type: boolean?
doc: Use positional consensus sequence when aligning high quality soft clipping
'sbg:x': 3001.30419921875
'sbg:y': 3575.3515625
- id: gatk_merge_bam_alignment_output_file_name
type: string?
doc: 'GATK MergeBamAlignment: Output File Name'
'sbg:x': 0
'sbg:y': 2134.53125
- id: fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex
type: boolean?
doc: >-
Fgbio FilterConsensusReads: Reverse [complement] per base tags on reverse
strand reads.- Simplex+Duplex
'sbg:x': 3467.848876953125
'sbg:y': 1974.3984375
- id: fgbio_filter_consensus_read_reverse_per_base_tags_duplex
type: boolean?
doc: >-
Fgbio FilterConsensusReads: Reverse [complement] per base tags on reverse
strand reads. - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 2081.1328125
- id: fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex
type: boolean?
doc: >-
Fgbio FilterConsensusReads: Mask (make N) consensus bases where the AB and
BA consensus reads disagree (for duplex-sequencing only).
'sbg:x': 3467.848876953125
'sbg:y': 2187.8671875
- id: fgbio_filter_consensus_read_require_single_strand_agreement_duplex
type: boolean?
doc: >-
Fgbio FilterConsensusReads: Mask (make N) consensus bases where the AB and
BA consensus reads disagree (for duplex-sequencing only).
'sbg:x': 3467.848876953125
'sbg:y': 2294.6015625
- id: fgbio_filter_consensus_read_max_base_error_rate_duplex
type: 'float[]?'
doc: >-
Fgbio FilterConsensusReads: The maximum error rate for a single consensus
base. (Max 3 values) - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 4109.0859375
- id: fgbio_filter_consensus_read_max_base_error_rate_simplex_duplex
type: 'float[]?'
doc: >-
Fgbio FilterConsensusReads: The maximum error rate for a single consensus
base. (Max 3 values) - Simplex + Duplex
'sbg:x': 3467.848876953125
'sbg:y': 4002.3515625
- id: fgbio_filter_consensus_read_max_no_call_fraction_duplex
type: float?
doc: >-
Fgbio FilterConsensusReads: Maximum fraction of no-calls in the read
after filtering - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3895.6171875
- id: fgbio_filter_consensus_read_max_read_error_rate_duplex
type: 'float[]?'
doc: >-
Fgbio FilterConsensusReads: The maximum raw-read error rate across the
entire consensus read. (Max 3 values) - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3682.1484375
- id: fgbio_filter_consensus_read_max_no_call_fraction_simplex_duplex
type: float?
doc: >-
Fgbio FilterConsensusReads: Maximum fraction of no-calls in the read
after filtering - Simplex + Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3788.8828125
- id: fgbio_filter_consensus_read_max_read_error_rate_simplex_duplex
type: 'float[]?'
doc: >-
The maximum raw-read error rate across the entire consensus read. (Max 3
values) - Simplex + Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3575.4140625
- id: fgbio_filter_consensus_read_min_base_quality_duplex
type: int?
doc: >-
Fgbio FilterConsensusReads: Mask (make N) consensus bases with quality
less than this threshold. - Dupelx
'sbg:x': 3467.848876953125
'sbg:y': 3468.6796875
- id: fgbio_filter_consensus_read_min_base_quality_simplex_duplex
type: int?
doc: >-
Fgbio FilterConsensusReads: Mask (make N) consensus bases with quality
less than this threshold. - Simplex + Dupelx
'sbg:x': 3467.848876953125
'sbg:y': 3361.9453125
- id: fgbio_filter_consensus_read_min_mean_base_quality_duplex
type: int?
doc: >-
Fgbio FilterConsensusReads: The minimum mean base quality across the
consensus read - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3255.2109375
- id: fgbio_filter_consensus_read_min_mean_base_quality_simplex_duplex
type: int?
doc: >-
Fgbio FilterConsensusReads: The minimum mean base quality across the
consensus read - Simplex + Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3148.4765625
- id: fgbio_filter_consensus_read_min_reads_duplex
type: 'int[]'
doc: >-
Fgbio FilterConsensusReads: The minimum number of reads supporting a
consensus base/read. (Max 3 values) - Duplex
'sbg:x': 3467.848876953125
'sbg:y': 3041.7421875
- id: fgbio_filter_consensus_read_min_reads_simplex_duplex
type: 'int[]'
doc: >-
Fgbio FilterConsensusReads: The minimum number of reads supporting a
consensus base/read. (Max 3 values) - Simplex+Duplex
'sbg:x': 3467.848876953125
'sbg:y': 2935.0078125
- id: fgbio_filter_consensus_read_output_file_name_simplex_duplex
type: string
doc: 'Fgbio FilterConsensusReads: Output file name Simplex + Duplex'
'sbg:x': 3467.848876953125
'sbg:y': 2401.3359375
- id: fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics
type: string?
doc: 'Fgbio FilterConsensusReads: Output file name Simplex alignment metrics'
'sbg:x': 3467.848876953125
'sbg:y': 2508.0703125
- id: fgbio_postprocessing_output_file_name_simplex
type: string
doc: 'Fgbio Postprocessing: Output file name Simplex'
'sbg:x': 3467.848876953125
'sbg:y': 1867.6640625
- id: fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics
type: string?
doc: 'Fgbio FilterConsensusReads: Output file name Duplex alignment metrics'
'sbg:x': 3467.848876953125
'sbg:y': 2614.8046875
- id: fgbio_filter_consensus_read_output_file_name_duplex
type: string
doc: 'Fgbio FilterConsensusReads: Output file name Duplex'
'sbg:x': 3467.848876953125
'sbg:y': 2721.5390625
- id: fgbio_filter_consensus_read_min_simplex_reads
type: int?
doc: >-
Fgbio FilterConsensusReads: The minimum number of reads supporting a
consensus base/read. (Max 3 values) - Simplex+Duplex
'sbg:x': 3467.848876953125
'sbg:y': 2828.2734375
- id: picard_addRG_read_group_sample_name
type: string
doc: 'PicardAddOrReplaceReadGroups: Read-Group sample name'
'sbg:x': 0
'sbg:y': 853.75
- id: bwa_number_of_threads
type: int?
doc: 'bwa mem: Number of threads'
'sbg:x': 0
'sbg:y': 5123.078125
- id: gatk_collect_alignment_summary_metrics_output_file_name
type: string?
doc: >-
GATK CollectAlignmentSummaryMetrics: Output file name for metrics on
collapsed BAM (Duplex+Simplex+Singletons)
'sbg:x': 0
'sbg:y': 2241.265625
- id: picard_addRG_sort_order
type: string
'sbg:x': 0
'sbg:y': 533.5625
- id: temporary_directory
type: string?
'sbg:x': 0
'sbg:y': 106.734375
- id: async_io
type: string?
'sbg:x': 0
'sbg:y': 5870.015625
outputs:
- id: fgbio_group_reads_by_umi_histogram
outputSource:
- fgbio_group_reads_by_umi_1_2_0/fgbio_group_reads_by_umi_histogram
type: File
'sbg:x': 1079.60107421875
'sbg:y': 2627.90625
- id: fgbio_collect_duplex_seq_metrics_umi_counts
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_umi_counts
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 2721.5390625
- id: fgbio_collect_duplex_seq_metrics_family_size
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_family_size
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 2828.2734375
- id: fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 2935.0078125
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts_txt
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_duplex_umi_counts
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 3041.7421875
- id: fgbio_collect_duplex_seq_metrics_duplex_qc
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_duplex_qc
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 3148.4765625
- id: fgbio_collect_duplex_seq_metrics_duplex_family_size
outputSource:
- >-
fgbio_collect_duplex_seq_metrics_1_2_0/fgbio_collect_duplex_seq_metrics_duplex_family_size
type: File
'sbg:x': 1680.5753173828125
'sbg:y': 3255.2109375
- id: gatk_sam_to_fastq_unpaired_fastq
outputSource:
- gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_unpaired_fastq
type: File?
'sbg:x': 2248.361328125
'sbg:y': 2581.5546875
- id: gatk_sam_to_fastq_second_end_fastq
outputSource:
- gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_second_end_fastq
type: File?
'sbg:x': 2248.361328125
'sbg:y': 2688.2890625
- id: gatk_sam_to_fastq_fastq
outputSource:
- gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_fastq
type: File?
'sbg:x': 2248.361328125
'sbg:y': 2795.0234375
- id: gatk_collect_alignment_summary_metrics_txt_simplex
outputSource:
- fgbio_separate_bams/gatk_collect_alignment_summary_metrics_txt_simplex
type: File
'sbg:x': 5103.671875
'sbg:y': 2668.171875
- id: gatk_collect_alignment_summary_metrics_txt_duplex
outputSource:
- fgbio_separate_bams/gatk_collect_alignment_summary_metrics_txt_duplex
type: File
'sbg:x': 5103.671875
'sbg:y': 2774.90625
- id: fgbio_postprocessing_simplex_bam
outputSource:
- fgbio_separate_bams/fgbio_postprocessing_simplex_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 5103.671875
'sbg:y': 2988.375
- id: fgbio_filter_consensus_reads_duplex_bam
outputSource:
- fgbio_separate_bams/fgbio_filter_consensus_reads_duplex_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 5103.671875
'sbg:y': 3201.84375
- id: fgbio_collapsed_bam
outputSource:
- indel_realignment/indel_realignment_bam
type: File
secondaryFiles:
- ^.bai
'sbg:x': 4160.3173828125
'sbg:y': 3230.7421875
- id: gatk_collect_alignment_summary_metrics_txt_collapsed
outputSource:
- >-
gatk_collect_alignment_summary_metrics_4_1_8_0/gatk_collect_alignment_summary_metrics_txt
type: File
'sbg:x': 5103.671875
'sbg:y': 2881.640625
- id: fgbio_group_reads_by_umi_bam
outputSource:
- fgbio_group_reads_by_umi_1_2_0/fgbio_group_reads_by_umi_bam
type: File
'sbg:x': 1079.60107421875
'sbg:y': 2734.640625
- id: fgbio_filter_consensus_reads_simplex_duplex_bam
outputSource:
- fgbio_separate_bams/fgbio_filter_consensus_reads_simplex_duplex_bam
type: File
'sbg:x': 5103.671875
'sbg:y': 3095.109375
steps:
- id: fgbio_group_reads_by_umi_1_2_0
in:
- id: input
source: fgbio_group_reads_by_umi_input
- id: output_file_name
source: fgbio_group_reads_by_umi_output_file_name
- id: family_size_histogram
source: fgbio_group_reads_by_umi_family_size_histogram
- id: raw_tag
source: fgbio_group_reads_by_umi_raw_tag
- id: assign_tag
source: fgbio_group_reads_by_umi_assign_tag
- id: include_non_pf_reads
source: fgbio_group_reads_by_umi_include_non_pf_reads
- id: strategy
source: fgbio_group_reads_by_umi_strategy
- id: edits
source: fgbio_group_reads_by_umi_edits
- id: min_umi_length
source: fgbio_group_reads_by_umi_min_umi_length
- id: temporary_directory
source: temporary_directory
- id: async_io
source: async_io
out:
- id: fgbio_group_reads_by_umi_bam
- id: fgbio_group_reads_by_umi_histogram
run: >-
command_line_tools/fgbio_group_reads_by_umi_1.2.0/fgbio_group_reads_by_umi_1.2.0.cwl
label: fgbio_group_reads_by_umi_1.2.0
'sbg:x': 541.75
'sbg:y': 2865.0078125
- id: fgbio_collect_duplex_seq_metrics_1_2_0
in:
- id: input
source: fgbio_group_reads_by_umi_1_2_0/fgbio_group_reads_by_umi_bam
- id: output_prefix
source: fgbio_collect_duplex_seq_metrics_output_prefix
- id: intervals
source: fgbio_collect_duplex_seq_metrics_intervals
- id: description
source: fgbio_collect_duplex_seq_metrics_description
- id: duplex_umi_counts
source: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
- id: min_ab_reads
source: fgbio_collect_duplex_seq_metrics_min_ab_reads
- id: min_ba_reads
source: fgbio_collect_duplex_seq_metrics_min_ba_reads
- id: mi_tag
source: fgbio_collect_duplex_seq_metrics_mi_tag
- id: temporary_directory
source: temporary_directory
- id: async_io
source: async_io
out:
- id: fgbio_collect_duplex_seq_metrics_family_size
- id: fgbio_collect_duplex_seq_metrics_duplex_family_size
- id: fgbio_collect_duplex_seq_metrics_duplex_yield_metrics
- id: fgbio_collect_duplex_seq_metrics_umi_counts
- id: fgbio_collect_duplex_seq_metrics_duplex_qc
- id: fgbio_collect_duplex_seq_metrics_duplex_umi_counts
run: >-
command_line_tools/fgbio_collect_duplex_seq_metrics_1.2.0/fgbio_collect_duplex_seq_metrics_1.2.0.cwl
label: fgbio_collect_duplex_seq_metrics_1.2.0
'sbg:x': 1079.60107421875
'sbg:y': 2904.375
- id: fgbio_call_duplex_consensus_reads_1_2_0
in:
- id: input
source: fgbio_group_reads_by_umi_1_2_0/fgbio_group_reads_by_umi_bam
- id: output_file_name
source: fgbio_call_duplex_consensus_reads_output_file_name
- id: read_name_prefix
source: fgbio_call_duplex_consensus_reads_read_name_prefix
- id: read_group_id
source: fgbio_call_duplex_consensus_reads_read_group_id
- id: error_rate_pre_umi
source: fgbio_call_duplex_consensus_reads_error_rate_pre_umi
- id: error_rate_post_umi
source: fgbio_call_duplex_consensus_reads_error_rate_post_umi
- id: min_input_base_quality
source: fgbio_call_duplex_consensus_reads_min_input_base_quality
- id: trim
source: fgbio_call_duplex_consensus_reads_trim
- id: sort_order
source: fgbio_call_duplex_consensus_reads_sort_order
- id: min_reads
source:
- fgbio_call_duplex_consensus_reads_min_reads
- id: max_reads_per_strand
source: fgbio_call_duplex_consensus_reads_max_reads_per_strand
- id: temporary_directory
source: temporary_directory
- id: async_io
source: async_io
out:
- id: fgbio_call_duplex_consensus_reads_bam
run: >-
command_line_tools/fgbio_call_duplex_consensus_reads_1.2.0/fgbio_call_duplex_consensus_reads_1.2.0.cwl
label: fgbio_call_duplex_consensus_reads_1.2.0
'sbg:x': 1079.60107421875
'sbg:y': 3158.109375
- id: gatk_sam_to_fastq_4_1_8_0
in:
- id: fastq
source: gatk_sam_to_fastq_output_name_R1
- id: input
source: >-
fgbio_call_duplex_consensus_reads_1_2_0/fgbio_call_duplex_consensus_reads_bam
- id: include_non_pf_reads
source: gatk_sam_to_fastq_include_non_pf_reads
- id: include_non_primary_alignments
source: gatk_sam_to_fastq_include_non_primary_alignments
- id: reference_sequence
source: reference_sequence
- id: second_end_fastq
source: gatk_sam_to_fastq_output_name_R2
- id: unpaired_fastq
source: gatk_sam_to_fastq_output_name_unpaired
- id: validation_stringency
source: validation_stringency
- id: temporary_directory
source: temporary_directory
out:
- id: gatk_sam_to_fastq_fastq
- id: gatk_sam_to_fastq_unpaired_fastq
- id: gatk_sam_to_fastq_second_end_fastq
run: command_line_tools/gatk_sam_to_fastq_4.1.8.0/gatk_sam_to_fastq_4.1.8.0.cwl
label: GATK-SamToFastq
'sbg:x': 1680.5753173828125
'sbg:y': 2558.8203125
- id: alignment
in:
- id: create_bam_index
source: create_bam_index
- id: output_file_name
source: picard_addRG_output_file_name
- id: read_group_description
source: picard_addRG_read_group_description
- id: read_group_identifier
source: picard_addRG_read_group_identifier
- id: read_group_library
source: picard_addRG_read_group_library
- id: read_group_platform_unit
source: picard_addRG_read_group_platform_unit
- id: read_group_run_date
source: picard_addRG_read_group_run_date
- id: read_group_sample_name
source: picard_addRG_read_group_sample_name
- id: read_group_sequencing_center
source: picard_addRG_read_group_sequencing_center
- id: read_group_sequencing_platform
source: picard_addRG_read_group_sequencing_platform
- id: sort_order
source: picard_addRG_sort_order
- id: validation_stringency
source: validation_stringency
- id: reference
source: reference_sequence
- id: reads
source:
- gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_fastq
- gatk_sam_to_fastq_4_1_8_0/gatk_sam_to_fastq_second_end_fastq
- id: output
source: bwa_mem_output
- id: P
source: bwa_mem_P
- id: M
source: bwa_mem_M
- id: T
source: bwa_mem_T
- id: 'Y'
source: bwa_mem_Y
- id: K
source: bwa_mem_K
- id: bwa_number_of_threads
source: bwa_number_of_threads
out:
- id: picard_add_or_replace_read_groups_bam
run: subworkflows/alignment/alignment.cwl
label: alignment
'sbg:x': 2248.361328125
'sbg:y': 3148.4609375
- id: indel_realignment
in:
- id: window_size
source: abra2_window_size
- id: soft_clip_contig
source: abra2_soft_clip_contig
- id: scoring_gap_alignments
source: abra2_scoring_gap_alignments
- id: reference_fasta
source: reference_sequence
- id: no_sort
source: abra2_no_sort
- id: maximum_mixmatch_rate
source: abra2_maximum_mixmatch_rate
- id: maximum_average_depth
source: abra2_maximum_average_depth
- id: input_bam
source: gatk_merge_bam_alignment_4_1_8_0/gatk_merge_bam_alignment_bam
- id: contig_anchor
source: abra2_contig_anchor
- id: consensus_sequence
source: abra2_consensus_sequence
- id: bam_index
source: create_bam_index
- id: option_bedgraph
source: bedtools_genomecov_option_bedgraph
- id: no_edge_complex_indel
source: abra2_no_edge_complex_indel
- id: distance_between_features
source: bedtools_merge_distance_between_features
- id: output_bams
source:
- abra2_output_bams
- id: validation_stringency
source: validation_stringency
- id: sort_order
source: sort_order
- id: output_file_name
source: picard_fixmate_information_output_file_name
- id: create_bam_index
source: create_bam_index
- id: temporary_directory
source: temporary_directory
out:
- id: indel_realignment_bam
run: subworkflows/indel_realignment/indel_realignment.cwl
label: indel_realignment
'sbg:x': 3467.848876953125
'sbg:y': 1627.9296875
- id: gatk_merge_bam_alignment_4_1_8_0
in:
- id: unmapped_bam
source: >-
fgbio_call_duplex_consensus_reads_1_2_0/fgbio_call_duplex_consensus_reads_bam
- id: reference
source: reference_sequence
- id: output_file_name
source: gatk_merge_bam_alignment_output_file_name
- id: aligned_bam
source:
- alignment/picard_add_or_replace_read_groups_bam
valueFrom: '${ return [ self ]; }'
- id: sort_order
source: sort_order
- id: validation_stringency
source: validation_stringency
- id: create_index
source: create_bam_index
- id: temporary_directory
source: temporary_directory
out:
- id: gatk_merge_bam_alignment_bam
run: >-
command_line_tools/gatk_merge_bam_alignment_4.1.8.0/gatk_merge_bam_alignment_4.1.8.0.cwl
label: GATK-MergeBamAlignment
'sbg:x': 3001.30419921875
'sbg:y': 2245.6796875
- id: fgbio_separate_bams
in:
- id: reference_fasta
source: reference_sequence
- id: input
source: indel_realignment/indel_realignment_bam
- id: reverse_per_base_tags_simplex_duplex
source: fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex
- id: require_single_strand_agreement_simplex_duplex
source: >-
fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex
- id: output_file_name_simplex_duplex
source: fgbio_filter_consensus_read_output_file_name_simplex_duplex
- id: min_reads_simplex_duplex
source:
- fgbio_filter_consensus_read_min_reads_simplex_duplex
- id: min_mean_base_quality_simplex_duplex
source: fgbio_filter_consensus_read_min_mean_base_quality_simplex_duplex
- id: max_base_error_rate_simplex_duplex
source:
- fgbio_filter_consensus_read_max_base_error_rate_simplex_duplex
- id: max_no_call_fraction_simplex_duplex
source: fgbio_filter_consensus_read_max_no_call_fraction_simplex_duplex
- id: min_base_quality_simplex_duplex
source: fgbio_filter_consensus_read_min_base_quality_simplex_duplex
- id: max_read_error_rate_simplex_duplex
source:
- fgbio_filter_consensus_read_max_read_error_rate_simplex_duplex
- id: reverse_per_base_tags_duplex
source: fgbio_filter_consensus_read_reverse_per_base_tags_duplex
- id: require_single_strand_agreement_duplex
source: fgbio_filter_consensus_read_require_single_strand_agreement_duplex