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
reference_sequence	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
validation_stringency	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.
create_bam_index	GATK: Generate BAM index file when possible
sort_order	GATK: The order in which the merged reads should be output.

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)
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
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.
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.
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.
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.

GATK SamToFastq

Argument Name	Summary	Default Value
gatk_sam_to_fastq_output_name_unpaired	unpaired fastq output file name
gatk_sam_to_fastq_output_name_R1	Read1 fastq.gz output file name
gatk_sam_to_fastq_output_name_R2	Read2 fastq.gz output file name
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.

BWA MEM

Argument Name	Summary	Default Value
bwa_mem_Y	Force soft-clipping rather than default hard-clipping of supplementary alignments
bwa_mem_T	Don’t output alignment with score lower than INT. This option only affects output.
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.
bwa_mem_output	Output SAM file name
bwa_mem_M	Mark shorter split hits as secondary
bwa_mem_K	to achieve deterministic alignment results (Note: this is a hidden option)
bwa_number_of_threads	Number of threads

Picard AddOrReplaceReadGroups

Argument Name	Summary	Default Value
picard_addRG_read_group_sequencing_platform	Read-Group platform (e.g. ILLUMINA, SOLID)
picard_addRG_read_group_sequencing_center	Read-Group sequencing center name
picard_addRG_read_group_run_date	Read-Group date in (Iso8601Date)
picard_addRG_read_group_platform_unit	Read-Group Platform Unit (eg. run barcode)
picard_addRG_read_group_library	Read-Group library
picard_addRG_read_group_identifier	Read-Group ID
picard_addRG_read_group_description	Read-Group Description
picard_addRG_output_file_name	Output BAM file name
picard_addRG_sort_order	Sort order for BAM file
picard_addRG_read_group_sample_name	Read-Group sample name

GATK MergeBamAlignment

Argument Name	Summary	Default Value
gatk_merge_bam_alignment_output_file_name	Output BAM file name

bedtools genomecov

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

bedtools merge

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

ABRA2

Argument Name	Summary	Default Value
abra2_window_size	Processing window size and overlap (size,overlap) (default: 400,200)
abra2_soft_clip_contig	Soft clip contig args [maxcontigs,min_base_qual,frac high_qual_bases,min_soft_clip_len] (default:16,13,80,15)
abra2_scoring_gap_alignments	Scoring used for contig alignments(match, mismatch_penalty,gap_open_penalty,gap_extend_penalty) (default:8,32,48,1)
abra2_no_sort	Do not attempt to sort final output
abra2_no_edge_complex_indel	Prevent output of complex indels at read start or read end
abra2_maximum_mixmatch_rate	Max allowed mismatch rate when mapping reads back to contigs (default: 0.05)
abra2_maximum_average_depth	Regions with average depth exceeding this value will be downsampled (default: 1000)
abra2_contig_anchor	Contig anchor [M_bases_at_contig_edge,max_mismatches_near_edge] (default:10,2)
abra2_consensus_sequence	Use positional consensus sequence when aligning high quality soft clipping

Picard FixMateInformation

Argument Name	Summary	Default Value
picard_fixmate_information_output_file_name	The output BAM file to write to

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. - Dupelx
fgbio_filter_consensus_read_min_base_quality_simplex_duplex	Mask (make N) consensus bases with quality less than this threshold. - Simplex+Dupelx
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
fgbio_filter_consensus_read_min_reads_simplex_duplex	The minimum number of reads supporting a consensus base/read. (Max 3 values) -Simplex+Duplex
fgbio_filter_consensus_read_output_file_name_simplex_duplex	Output BAM file name Simplex + Duplex
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
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

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.json

{
    "abra2_consensus_sequence": null,
    "abra2_contig_anchor": null,
    "abra2_maximum_average_depth": null,
    "abra2_maximum_mixmatch_rate": null,
    "abra2_no_edge_complex_indel": true,
    "abra2_no_sort": null,
    "abra2_output_bams": "collapsed_abra.bam",
    "abra2_scoring_gap_alignments": null,
    "abra2_soft_clip_contig": null,
    "abra2_window_size": null,
    "bedtools_genomecov_option_bedgraph": true,
    "bedtools_merge_distance_between_features": null,
    "bwa_mem_K": 1000000,
    "bwa_mem_M": null,
    "bwa_mem_P": null,
    "bwa_mem_T": 30,
    "bwa_mem_Y": true,
    "bwa_mem_output": "test_collapsed_alignment.sam",
    "bwa_number_of_threads": null,
    "create_bam_index": true,
    "fgbio_call_duplex_consensus_reads_error_rate_post_umi": null,
    "fgbio_call_duplex_consensus_reads_error_rate_pre_umi": null,
    "fgbio_call_duplex_consensus_reads_max_reads_per_strand": null,
    "fgbio_call_duplex_consensus_reads_min_input_base_quality": null,
    "fgbio_call_duplex_consensus_reads_min_reads": [
        1,
        1,
        0
    ],
    "fgbio_call_duplex_consensus_reads_output_file_name": null,
    "fgbio_call_duplex_consensus_reads_read_group_id": "test",
    "fgbio_call_duplex_consensus_reads_read_name_prefix": null,
    "fgbio_call_duplex_consensus_reads_sort_order": null,
    "fgbio_call_duplex_consensus_reads_trim": null,
    "fgbio_collect_duplex_seq_metrics_description": null,
    "fgbio_collect_duplex_seq_metrics_duplex_umi_counts": true,
    "fgbio_collect_duplex_seq_metrics_intervals": null,
    "fgbio_collect_duplex_seq_metrics_mi_tag": null,
    "fgbio_collect_duplex_seq_metrics_min_ab_reads": null,
    "fgbio_collect_duplex_seq_metrics_min_ba_reads": null,
    "fgbio_collect_duplex_seq_metrics_output_prefix": null,
    "fgbio_filter_consensus_read_max_base_error_rate_duplex": null,
    "fgbio_filter_consensus_read_max_base_error_rate_simplex_duplex": null,
    "fgbio_filter_consensus_read_max_no_call_fraction_duplex": null,
    "fgbio_filter_consensus_read_max_no_call_fraction_simplex_duplex": null,
    "fgbio_filter_consensus_read_max_read_error_rate_duplex": null,
    "fgbio_filter_consensus_read_max_read_error_rate_simplex_duplex": null,
    "fgbio_filter_consensus_read_min_base_quality_duplex": 30,
    "fgbio_filter_consensus_read_min_base_quality_simplex_duplex": 30,
    "fgbio_filter_consensus_read_min_mean_base_quality_duplex": null,
    "fgbio_filter_consensus_read_min_mean_base_quality_simplex_duplex": null,
    "fgbio_filter_consensus_read_min_reads_duplex": [
        2,
        1,
        1
    ],
    "fgbio_filter_consensus_read_min_reads_simplex_duplex": [
        3,
        3,
        0
    ],
    "fgbio_filter_consensus_read_min_simplex_reads": null,
    "fgbio_filter_consensus_read_output_file_name_duplex": "collapsed_duplex.bam",
    "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": "collapsed_simplex-duplex.bam",
    "fgbio_filter_consensus_read_require_single_strand_agreement_duplex": true,
    "fgbio_filter_consensus_read_require_single_strand_agreement_simplex_duplex": null,
    "fgbio_filter_consensus_read_reverse_per_base_tags_duplex": true,
    "fgbio_filter_consensus_read_reverse_per_base_tags_simplex_duplex": true,
    "fgbio_group_reads_by_umi_assign_tag": null,
    "fgbio_group_reads_by_umi_edits": null,
    "fgbio_group_reads_by_umi_family_size_histogram": "group_reads_umi.hist.txt",
    "fgbio_group_reads_by_umi_include_non_pf_reads": null,
    "fgbio_group_reads_by_umi_input": {
        "class": "File",
        "path": "/Users/shahr2/Documents/test_reference/Uncollapsed_BAM_Generation_Output/test_fx.bam"
    },
    "fgbio_group_reads_by_umi_min_umi_length": null,
    "fgbio_group_reads_by_umi_output_file_name": null,
    "fgbio_group_reads_by_umi_raw_tag": null,
    "fgbio_group_reads_by_umi_strategy": "paired",
    "fgbio_postprocessing_output_file_name_simplex": "collapsed_simplex.bam",
    "gatk_collect_alignment_summary_metrics_output_file_name": null,
    "gatk_merge_bam_alignment_output_file_name": null,
    "gatk_sam_to_fastq_include_non_pf_reads": null,
    "gatk_sam_to_fastq_include_non_primary_alignments": null,
    "gatk_sam_to_fastq_output_name_R1": "test_fx_group_cons_R1.fastq.gz",
    "gatk_sam_to_fastq_output_name_R2": "test_fx_group_cons_R2.fastq.gz",
    "gatk_sam_to_fastq_output_name_unpaired": null,
    "picard_addRG_sort_order": "queryname",
    "picard_addRG_output_file_name": null,
    "picard_addRG_read_group_description": null,
    "picard_addRG_read_group_identifier": "test",
    "picard_addRG_read_group_library": "test",
    "picard_addRG_read_group_platform_unit": "IDT11",
    "picard_addRG_read_group_run_date": null,
    "picard_addRG_read_group_sample_name": "MSKCC",
    "picard_addRG_read_group_sequencing_center": "ILLUMINA",
    "picard_addRG_read_group_sequencing_platform": "test",
    "picard_fixmate_information_output_file_name": "collapsed_fx.bam",
    "reference_sequence": {
        "class": "File",
        "path": "/Users/shahr2/Documents/test_reference/test_uncollapsed_bam_generation/reference/chr14_chr16.fasta"
    },
    "sort_order": "coordinate",
    "validation_stringency": "LENIENT"
}