Inputs Description
Input files and parameters required to run workflow
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Input files and parameters required to run workflow
Last updated
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Common workflow language execution engines accept two types of input that are or , please make sure to use one of these while generating the input file. For more information refer to:
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.
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
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.
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.
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.
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
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
Argument Name
Summary
Default Value
gatk_merge_bam_alignment_output_file_name
Output BAM file name
Argument Name
Summary
Default Value
bedtools_genomecov_option_bedgraph
option flag parameter to choose output file format. -bg refers to bedgraph format
Argument Name
Summary
Default Value
bedtools_merge_distance_between_features
Maximum distance between features allowed for features to be merged.
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
Argument Name
Summary
Default Value
picard_fixmate_information_output_file_name
The output BAM file to write to
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
Argument Name
Summary
Default Value
fgbio_postprocessing_output_file_name_simplex
Output BAM file name Simplex
Argument Name
Summary
Default Value
gatk_collect_alignment_summary_metrics_output_file_name
Output file name for metrics on collapsed BAM (Duplex+Simplex+Singletons)