Inputs Description

Input files and parameters required to run workflow

Common workflow language execution engines accept two types of input that are JSON or YAML, please make sure to use one of these while generating the input file. For more information refer to: http://www.commonwl.org/user_guide/yaml/

Parameter Used by Tools

Common Parameters Across Tools

Argument Name	Summary	Default Value
sequencing-center	The sequencing center from which the data originated	MSKCC
sample	The name of the sequenced sample.(Required)
run-date	Date the run was produced, to insert into the read group header (Iso8601Date)
read-group-id	Read group ID to use in the file header (Required)
platform-unit	Read-Group Platform Unit (eg. run barcode) (Required)
platform-model	Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)	novaseq
platform	Read-Group platform (e.g. ILLUMINA, SOLID).	ILLUMINA
library	The name/ID of the sequenced library. (Required)
description	Description of the read group.
comment	Comments to include in the output file’s header.
validation_stringency	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. The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values: STRICT or LENIENT or SILENT	LENIENT
sort_order	GATK: The order in which the reads should be output.
create_bam_index	GATK: Generate BAM index file when possible
reference_sequence	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
temporary_directory	Temporary directory to be used for all steps
fgbio_async_io	Fgbio asynchronous execution

Uncollapsed BAM Generation

Fgbio FastqToBam

Argument Name	Summary	Default Value
fgbio_fastq_to_bam_umi-tag	Tag in which to store molecular barcodes/UMIs.
fgbio_fastq_to_bam_sort	If true, query-name sort the BAM file, otherwise preserve input order.
fgbio_fastq_to_bam_input	Fastq files corresponding to each sequencing read ( e.g. R1, I1, etc.). Please refer to the template file to get this correct.
read-structures	Read structures, one for each of the FASTQs. Refer to the tool for more details
fgbio_fastq_to_bam_predicted-insert-size	Predicted median insert size, to insert into the read group header
fgbio_fastq_to_bam_output_file_name	The output SAM or BAM file to be written.

Picard MergeSamFiles

Argument Name	Summary	Default Value
gatk_merge_sam_files_output_file_name	SAM or BAM file to write the merged result to (Required)
merge_sam_files_sort_order	Sort order of output file	queryname

Picard SamToFastq

Argument Name	Summary	Default Value
unpaired_fastq_file	unpaired fastq output file name
UBG_picard_SamToFastq_R1_output_fastq	Read1 fastq.gz output file name for uncollapsed bam generation (Required)
UBG_picard_SamToFastq_R2_output_fastq	Read2 fastq.gz output file name for uncollapsed bam generation (Required)
BC_gatk_sam_to_fastq_output_name_R1	Read1 fastq.gz output file name for bam collapsing (Required)
BC_gatk_sam_to_fastq_output_name_R2	Read2 fastq.gz output file name for bam collapsing (Required)
gatk_sam_to_fastq_include_non_primary_alignments	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.
gatk_sam_to_fastq_include_non_pf_reads	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.

Fastp

Argument Name	Summary	Default Value
fastp_unpaired1_output_file_name	For PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it.
fastp_unpaired2_output_file_name	For PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --unpaired1 (default mode), both unpaired reads will be written to this same file.
fastp_read1_adapter_sequence	the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.	GATCGGAAGAGC
fastp_read2_adapter_sequence	The adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as (string)	AGATCGGAAGAGC
fastp_read1_output_file_name	Read1 output File Name (Required)
fastp_read2_output_file_name	Read2 output File Name (Required)
fastp_minimum_read_length	reads shorter than length_required will be discarded	25
fastp_json_output_file_name	the json format report file name (Required)
fastp_html_output_file_name	the html format report file name (Required)
disable_trim_poly_g	Disable Poly-G trimming.	True
disable_quality_filtering	Disable base quality filtering.	True

BWA MEM

Argument Name	Summary	Default Value
bwa_mem_Y	Force soft-clipping rather than default hard-clipping of supplementary alignments	True
bwa_mem_T	Don’t output alignment with score lower than INT. This option only affects output.	30
bwa_mem_P	In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.
UBG_bwa_mem_output	Output SAM file name for uncollapsed bam generation (Required)
BC_bwa_mem_output	Output SAM file name for bam collapsing (Required)
bwa_mem_M	Mark shorter split hits as secondary
bwa_mem_K	to achieve deterministic alignment results (Note: this is a hidden option)	1000000
bwa_number_of_threads	Number of threads

Picard AddOrReplaceReadGroups

Argument Name	Summary	Default Value
UBG_picard_addRG_output_file_name	Output BAM file name for uncollapsed bam generation (Required)
BC_picard_addRG_output_file_name	Output BAM file name for bam collapsing (Required)
picard_addRG_sort_order	Sort order for the BAM file	queryname

GATK MergeBamAlignment

Argument Name	Summary	Default Value
UBG_gatk_merge_bam_alignment_output_file_name	Output BAM file name for uncollapsed bam generation (Required)
BC_gatk_merge_bam_alignment_output_file_name	Output BAM file name for bam collapsing (Required)

Picard MarkDuplicates

Argument Name	Summary	Default Value
optical_duplicate_pixel_distance	The maximum offset between two duplicate clusters in order to consider them optical duplicates. The default is appropriate for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is more appropriate. For other platforms and models, users should experiment to find what works best.	2500
read_name_regex	Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.
duplicate_scoring_strategy	The scoring strategy for choosing the non-duplicate among candidates.
gatk_mark_duplicates_output_file_name	The output file to write marked records to (Required)
gatk_mark_duplicates_duplication_metrics_file_name	File to write duplication metrics to (Required)
gatk_mark_duplicates_assume_sort_order	If not null, assume that the input file has this order even if the header says otherwise.

bedtools genomecov

Argument Name	Summary	Default Value
bedtools_genomecov_option_bedgraph	option flag parameter to choose output file format. -bg refers to bedgraph format	True

bedtools merge

Argument Name	Summary	Default Value
bedtools_merge_distance_between_features	Maximum distance between features allowed for features to be merged.	10

ABRA2

Argument Name	Summary	Default Value
abra2_window_size	Processing window size and overlap (size,overlap)	"400,200"
abra2_soft_clip_contig	Soft clip contig args [maxcontigs,min_base_qual,frac high_qual_bases,min_soft_clip_len]	"16,13,80,15"
abra2_scoring_gap_alignments	Scoring used for contig alignments(match, mismatch_penalty,gap_open_penalty,gap_extend_penalty)	"8,32,48,1"
abra2_no_sort	Do not attempt to sort final output	True
abra2_no_edge_complex_indel	Prevent output of complex indels at read start or read end	True
abra2_maximum_mixmatch_rate	Max allowed mismatch rate when mapping reads back to contigs	0.1
abra2_maximum_average_depth	Regions with average depth exceeding this value will be down-sampled	1000
abra2_contig_anchor	Contig anchor [M_bases_at_contig_edge,max_mismatches_near_edge]	"10,2"
abra2_consensus_sequence	Use positional consensus sequence when aligning high quality soft clipping
BC_abra2_output_bams	The output BAM file to write to (Required)
UBG_abra2_output_bams	The output BAM file to write to (Required)

Picard FixMateInformation

Argument Name	Summary	Default Value
UBG_picard_fixmateinformation_output_file_name	The output BAM file to write to for uncollapsed bam generation (Required)
BC_picard_fixmate_information_output_file_name	The output BAM file to write to for bam collapsing (Required)

Base Quality Score Recalibration

GATK BaseRecalibrator

Argument Name	Summary	Default Value
gatk_base_recalibrator_known_sites	One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis (Required)
gatk_bqsr_read_filter	Read filters to be applied before analysis
base_recalibrator_output_file_name	The output recalibration table file to create (Required)

GATK ApplyBQSR

Argument Name	Summary	Default Value
apply_bqsr_output_file_name	The output BAM file (Required)
gatk_bqsr_disable_read_filter	Read filters to be disabled before analysis

Collapsed BAM Generation

Fgbio GroupReadsByUmi

Argument Name	Summary	Default Value
fgbio_group_reads_by_umi_input	The input BAM file
fgbio_group_reads_by_umi_strategy	The UMI assignment strategy. (identity, edit, adjacency, paired)	paired
fgbio_group_reads_by_umi_raw_tag	The tag containing the raw UMI.	RX
fgbio_group_reads_by_umi_output_file_name	The output BAM file name (Required)
fgbio_group_reads_by_umi_min_umi_length	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.
fgbio_group_reads_by_umi_include_non_pf_reads	Include non-PF reads.	False
fgbio_group_reads_by_umi_family_size_histogram	Optional output of tag family size counts. (Required)	Give a file name. ex: samplename.hist
fgbio_group_reads_by_umi_edits	The allowable number of edits between UMIs.	1
fgbio_group_reads_by_umi_assign_tag	The output tag for UMI grouping.	MI

Fgbio CollectDuplexSeqMetrics

Argument Name	Summary	Default Value
fgbio_collect_duplex_seq_metrics_intervals	Optional set of intervals over which to restrict analysis.
fgbio_collect_duplex_seq_metrics_output_prefix	Prefix of output files to write.
fgbio_collect_duplex_seq_metrics_min_ba_reads	Minimum BA reads to call a tag family a ‘duplex’.
fgbio_collect_duplex_seq_metrics_min_ab_reads	Minimum AB reads to call a tag family a ‘duplex’.
fgbio_collect_duplex_seq_metrics_mi_tag	The output tag for UMI grouping.	MI
fgbio_collect_duplex_seq_metrics_duplex_umi_counts	If true, produce the .duplex_umi_counts.txt file with counts of duplex UMI observations.	True
fgbio_collect_duplex_seq_metrics_description	Description of data set used to label plots. Defaults to sample/library.

Fgbio CallDuplexConsensusReads

Argument Name	Summary	Default Value
fgbio_call_duplex_consensus_reads_trim	If true, quality trim input reads in addition to masking low Q bases.
fgbio_call_duplex_consensus_reads_sort_order	The sort order of the output, if :none: then the same as the input.
fgbio_call_duplex_consensus_reads_read_name_prefix	The prefix all consensus read names
fgbio_call_duplex_consensus_reads_read_group_id	The new read group ID for all the consensus reads.
fgbio_call_duplex_consensus_reads_output_file_name	Output SAM or BAM file to write consensus reads.
fgbio_call_duplex_consensus_reads_min_reads	The minimum number of input reads to a consensus read.	1 1 0
fgbio_call_duplex_consensus_reads_min_input_base_quality	Ignore bases in raw reads that have Q below this value.
fgbio_call_duplex_consensus_reads_max_reads_per_strand	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.
fgbio_call_duplex_consensus_reads_error_rate_pre_umi	The Phred-scaled error rate for an error prior to the UMIs being integrated.
fgbio_call_duplex_consensus_reads_error_rate_post_umi	The Phred-scaled error rate for an error post the UMIs have been integrated.

Fgbio FilterConsensusReads

Argument Name	Summary	Default Value
fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex	Reverse [complement] per base tags on reverse strand reads.- Simplex+Duplex
fgbio_filter_consensus_read_reverse_per_base_tags_duplex	Reverse [complement] per base tags on reverse strand reads. - Duplex
fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex	Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).
fgbio_filter_consensus_read_require_single_strand_agreement_duplex	Mask (make N) consensus bases where the AB and BA consensus reads disagree (for duplex-sequencing only).
fgbio_filter_consensus_read_max_base_error_rate_duplex	The maximum error rate for a single consensus base. (Max 3 values) - Duplex
fgbio_filter_consensus_read_max_base_error_rate_simplex_duplex	The maximum error rate for a single consensus base. (Max 3 values) - Simplex + Duplex
fgbio_filter_consensus_read_max_no_call_fraction_duplex	Maximum fraction of no-calls in the read after filtering - Duplex
fgbio_filter_consensus_read_max_read_error_rate_duplex	The maximum raw-read error rate across the entire consensus read. (Max 3 values) - Duplex
fgbio_filter_consensus_read_max_no_call_fraction_simplex_duplex	Maximum fraction of no- calls in the read after filtering - Simplex + Duplex
fgbio_filter_consensus_read_max_read_error_rate_simplex_duplex	The maximum raw-read error rate across the entire consensus read. (Max 3 values) - Simplex + Duplex
fgbio_filter_consensus_read_min_base_quality_duplex	Mask (make N) consensus bases with quality less than this threshold. - Duplex
fgbio_filter_consensus_read_min_base_quality_simplex_duplex	Mask (make N) consensus bases with quality less than this threshold. - Simplex+Duplex
fgbio_filter_consensus_read_min_mean_base_quality_duplex	The minimum mean base quality across the consensus read - Duplex
fgbio_filter_consensus_read_min_mean_base_quality_simplex_duplex	The minimum mean base quality across the consensus read - Simplex + Duplex
fgbio_filter_consensus_read_min_reads_duplex	The minimum number of reads supporting a consensus base/read. (Max 3 values) - Duplex	2, 1, 1
fgbio_filter_consensus_read_min_reads_simplex_duplex	The minimum number of reads supporting a consensus base/read. (Max 3 values) - Simplex+Duplex	3, 3, 0
fgbio_filter_consensus_read_output_file_name_simplex_duplex	Output BAM file name Simplex + Duplex (Required)
fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics	Output file name Duplex alignment metrics
fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics	Output file name Simplex alignment metrics
fgbio_filter_consensus_read_output_file_name_duplex	Output BAM file name - Duplex (Required)
fgbio_filter_consensus_read_min_simplex_reads	The minimum number of reads supporting a consensus base/read. (Max 3 values) - Simplex+Duplex

Fgbio Postprocessing

Argument Name	Summary	Default Value
fgbio_postprocessing_output_file_name_simplex	Output BAM file name Simplex (Required)

Picard CollectAlignmentSummaryMetrics

Argument Name	Summary	Default Value
gatk_collect_alignment_summary_metrics_output_file_name	Output file name for metrics on collapsed BAM (Duplex+Simplex+Singletons)

Template Inputs File

inputs.yaml

BC_abra2_output_bams: null
BC_bwa_mem_output: null
BC_gatk_merge_bam_alignment_output_file_name: null
BC_gatk_sam_to_fastq_output_name_R1: null
BC_gatk_sam_to_fastq_output_name_R2: null
BC_picard_addRG_output_file_name: null
BC_picard_fixmate_information_output_file_name: null
UBG_abra2_output_bams: null
UBG_bwa_mem_output: null
UBG_gatk_merge_bam_alignment_output_file_name: null
UBG_picard_SamToFastq_R1_output_fastq: null
UBG_picard_SamToFastq_R2_output_fastq: null
UBG_picard_addRG_output_file_name: null
UBG_picard_fixmateinformation_output_file_name: null
abra2_bam_index: null
abra2_consensus_sequence: null
abra2_contig_anchor: null
abra2_maximum_average_depth: null
abra2_maximum_mixmatch_rate: null
abra2_no_edge_complex_indel: null
abra2_scoring_gap_alignments: null
abra2_soft_clip_contig: null
abra2_window_size: null
apply_bqsr_output_file_name: null
base_recalibrator_output_file_name: null
bedtools_genomecov_option_bedgraph: null
bedtools_merge_distance_between_features: null
bwa_mem_K: null
bwa_mem_T: null
bwa_mem_Y: null
create_bam_index: null
fastp_html_output_file_name: null
fastp_json_output_file_name: null
fastp_minimum_read_length: null
fastp_read1_adapter_sequence: null
fastp_read1_output_file_name: null
fastp_read2_adapter_sequence: null
fastp_read2_output_file_name: null
fgbio_async_io: null
fgbio_call_duplex_consensus_reads_min_reads: null
fgbio_call_duplex_consensus_reads_output_file_name: null
fgbio_collect_duplex_seq_metrics_duplex_umi_counts: null
fgbio_collect_duplex_seq_metrics_intervals: null
fgbio_collect_duplex_seq_metrics_output_prefix: null
fgbio_fastq_to_bam_input: null
fgbio_filter_consensus_read_min_base_quality_duplex: null
fgbio_filter_consensus_read_min_base_quality_simplex_duplex: null
fgbio_filter_consensus_read_min_reads_duplex: null
fgbio_filter_consensus_read_min_reads_simplex_duplex: null
fgbio_filter_consensus_read_output_file_name_duplex: null
fgbio_filter_consensus_read_output_file_name_duplex_aln_metrics: null
fgbio_filter_consensus_read_output_file_name_simplex_aln_metrics: null
fgbio_filter_consensus_read_output_file_name_simplex_duplex: null
fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex: null
fgbio_group_reads_by_umi_family_size_histogram: null
fgbio_group_reads_by_umi_output_file_name: null
fgbio_group_reads_by_umi_strategy: null
fgbio_postprocessing_output_file_name_simplex: null
gatk_base_recalibrator_add_output_sam_program_record: null
gatk_base_recalibrator_known_sites:
  - class: File
    metadata: {}
    path: >-
      /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/dbsnp_137_14_16.b37.vcf
    secondaryFiles:
      - class: File
        path: >-
          /Users/shahr2/Documents/test_reference/test_nucleo/known_sites/dbsnp_137_14_16.b37.vcf.idx
  - class: File
    metadata: {}
    path: >-
      /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf
    secondaryFiles:
      - class: File
        path: >-
          /Users/shahr2/Documents/test_reference/test_fastq_to_bam/known_sites/Mills_and_1000G_gold_standard-14_16.indels.b37.vcf.idx
gatk_collect_alignment_summary_metrics_output_file_name: null
gatk_mark_duplicates_duplication_metrics_file_name: null
gatk_mark_duplicates_output_file_name: null
gatk_merge_sam_files_output_file_name: null
library: null
merge_sam_files_sort_order: null
optical_duplicate_pixel_distance: null
picard_addRG_sort_order: null
platform: null
platform-model: null
platform-unit: null
read-group-id: null
read-structures: null
reference_sequence:
  class: File
  metadata: {}
  path: /Users/shahr2/Documents/test_reference/fasta/chr14_chr16.fasta
  secondaryFiles:
    - class: File
      path: ../../test_reference/fasta/chr14_chr16.fasta.amb
    - class: File
      path: ../../test_reference/fasta/chr14_chr16.fasta.ann
run-date: null
sample: null
sequencing-center: null
sort_order: null
temporary_directory: null
validation_stringency: null