Inputs Description

Various parameters required to run the 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
sample	The name of the sequenced sample.
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
platform-unit	Read-Group Platform Unit (eg. run barcode)
platform-model	Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)
platform	Read-Group platform (e.g. ILLUMINA, SOLID).
library	The name/ID of the sequenced library.
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
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

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
merge_sam_files_sort_order	Sort order of output file

Picard SamToFastq

Argument Name	Summary	Default Value
unpaired_fastq_file	unpaired fastq output file name
R1_output_fastq	Read1 fastq.gz output file name
R2_output_fastq	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.

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.
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	1
fastp_read2_output_file_name	Read2 output File Name
fastp_minimum_read_length	reads shorter than length_required will be discarded	15
fastp_json_output_file_name	the json format report file name
fastp_html_output_file_name	the html format report file name
fastp_failed_reads_output_file_name	specify the file to store reads that cannot pass the filters.

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_output_file_name	Output BAM file name
picard_addRG_sort_order	Sort order for the BAM file

GATK MergeBamAlignment

Argument Name	Summary	Default Value
gatk_merge_bam_alignment_output_file_name	Output BAM file name

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.
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
gatk_mark_duplicates_duplication_metrics_file_name	File to write duplication metrics to
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

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

Template inputs file

Parameters not marked as optional are required

template-inputs.json

{
    "R1_output_fastq": "processed_fastq_R1.fastq.gz",
    "R2_output_fastq": "processed_fastq_R2.fastq.gz",
    "abra2_bam_index": true,
    "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": "test_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_alignment.sam",
    "bwa_number_of_threads": null,
    "comment": null,
    "create_bam_index": true,
    "description": null,
    "duplicate_scoring_strategy": null,
    "fastp_failed_reads_output_file_name": null,
    "fastp_html_output_file_name": "test_fastp_out.html",
    "fastp_json_output_file_name": "test_fastp_out.json",
    "fastp_minimum_read_length": 25,
    "fastp_read1_adapter_sequence": "GATCGGAAGAGC",
    "fastp_read1_output_file_name": "trimmed_fastp_R1.fastq.gz",
    "fastp_read2_adapter_sequence": "AGATCGGAAGAGC",
    "fastp_read2_output_file_name": "trimmed_fastp_R2.fastq.gz",
    "fastp_unpaired1_output_file_name": null,
    "fastp_unpaired2_output_file_name": null,
    "fgbio_fastq_to_bam_input": [
[
        {
            "class": "File",
            "path": "/Users/shahr2/Documents/test_reference/seracare_0-5_R1_001ad.fastq.gz"
        },
        {
            "class": "File",
            "path": "/Users/shahr2/Documents/test_reference/seracare_0-5_R2_001ad.fastq.gz"
        }
],
[
        {
            "class": "File",
            "path": "/Users/shahr2/Documents/test_reference/seracare_0-5_R1_001ae.fastq.gz"
        },
        {
            "class": "File",
            "path": "/Users/shahr2/Documents/test_reference/seracare_0-5_R2_001ae.fastq.gz"
        }
]
    ],
    "fgbio_fastq_to_bam_output_file_name": null,
    "fgbio_fastq_to_bam_predicted-insert-size": null,
    "fgbio_fastq_to_bam_sort": null,
    "fgbio_fastq_to_bam_umi-tag": null,
    "gatk_mark_duplicates_assume_sort_order": null,
    "gatk_mark_duplicates_duplication_metrics_file_name": "test_dup_metrics.txt",
    "gatk_mark_duplicates_output_file_name": null,
    "gatk_merge_bam_alignment_output_file_name": null,
    "gatk_merge_sam_files_output_file_name": "test_unmapped.sam",
    "gatk_sam_to_fastq_include_non_pf_reads": null,
    "gatk_sam_to_fastq_include_non_primary_alignments": null,
    "library": "test",
    "merge_sam_files_sort_order": "queryname",
    "optical_duplicate_pixel_distance": 1500,
    "picard_addRG_sort_order": "queryname",
    "picard_addRG_output_file_name": "test_addRG.bam",
    "picard_fixmateinformation_output_file_name": "test_fx.bam",
    "platform": "ILLUMINA",
    "platform-model": "novaseq",
    "platform-unit": "IDT11",
    "read-group-id": "test",
    "read-structures": [
        "3M2S+T",
        "3M2S+T"
    ],
    "read_name_regex": null,
    "reference_sequence": {
        "class": "File",
        "metadata": {},
        "path": "/Users/shahr2/Documents/test_reference/test_uncollapsed_bam_generation/reference/chr14_chr16.fasta",
        "secondaryFiles": []
    },
    "run-date": null,
    "sample": "test",
    "sequencing-center": "MSKCC",
    "sort_order": "coordinate",
    "unpaired_fastq_file": null,
    "validation_stringency": "LENIENT"
}

Note that the paths in the inputs file are relative to the file itself. It is normally easier to use absolute paths whenever possible.